I mean as pafkata said I want to change the Cut/Copy/paste using the GUI. I want the layout mapping to behave exactly as Dvomak when I hit the Ctrl and not like QWERTY. Besides arguing which mapping is better, mine or QWERTY, I noticed that when I build a layout over QWRTY, which means the layout acts like QWERTY when CTRL is hit, some programs like word 2007 and acrobat revert to using my layout mapping(dvomak) instead of QWERTY when I hit the control although the layout is built over QWERTY and I have to remember the Cut/Copy/paste for both layouts instead of one. There is no problem when I do the mapping using Autohotkey, the problem only happens when I build my layout over QWERTY layout or even from scratch, where the behavior of QWERTY is still maintained when you hit CTRL
You said I should edit the files to accomplish this! which files, you mean the .klc. Should I open that and edit it. If so, I took a look inside the contents of the file and I will try to play with it for a while and see what I can do 
to swap the shifts, backspace, etc if possible... but I could not see anything that would achieve what I mentioned above.
KBD    Dvomak    "Dvomak-En"
COPYRIGHT    "(c) nimbostratue"
COMPANY    "my company"
LOCALENAME    "en-US"
LOCALEID    "00000409"
VERSION    1.0
SHIFTSTATE
0    //Column 4
1    //Column 5 : Shft
2    //Column 6 :       Ctrl
LAYOUT        ;an extra '@' at the end is a dead key
//SC    VK_        Cap    0    1    2
//--    ----        ----    ----    ----    ----
02    1        0    1    1    -1        // DIGIT ONE, DIGIT ONE, <none>
03    2        0    2    2    -1        // DIGIT TWO, DIGIT TWO, <none>
04    3        0    3    3    -1        // DIGIT THREE, DIGIT THREE, <none>
05    4        0    4    4    -1        // DIGIT FOUR, DIGIT FOUR, <none>
06    5        0    5    -1    -1        // DIGIT FIVE, <none>, <none>
07    6        0    6    -1    -1        // DIGIT SIX, <none>, <none>
08    7        0    7    -1    -1        // DIGIT SEVEN, <none>, <none>
09    8        0    8    -1    -1        // DIGIT EIGHT, <none>, <none>
0a    9        0    9    -1    -1        // DIGIT NINE, <none>, <none>
0b    0        0    0    -1    -1        // DIGIT ZERO, <none>, <none>
0c    OEM_MINUS    0    002d    -1    -1        // HYPHEN-MINUS, <none>, <none>
0d    OEM_PLUS    0    003d    -1    -1        // EQUALS SIGN, <none>, <none>
10    Q        0    0027    0027    -1        // APOSTROPHE, APOSTROPHE, <none>
11    W        0    002c    002c    -1        // COMMA, COMMA, <none>
12    E        1    u    U    -1        // LATIN SMALL LETTER U, LATIN CAPITAL LETTER U, <none>
13    R        1    g    G    -1        // LATIN SMALL LETTER G, LATIN CAPITAL LETTER G, <none>
14    T        1    k    K    -1        // LATIN SMALL LETTER K, LATIN CAPITAL LETTER K, <none>
15    Y        1    p    P    -1        // LATIN SMALL LETTER P, LATIN CAPITAL LETTER P, <none>
16    U        1    f    F    -1        // LATIN SMALL LETTER F, LATIN CAPITAL LETTER F, <none>
17    I        1    c    C    -1        // LATIN SMALL LETTER C, LATIN CAPITAL LETTER C, <none>
18    O        1    r    R    -1        // LATIN SMALL LETTER R, LATIN CAPITAL LETTER R, <none>
19    P        1    l    L    -1        // LATIN SMALL LETTER L, LATIN CAPITAL LETTER L, <none>
1a    OEM_4        0    005b    005b    -1        // LEFT SQUARE BRACKET, LEFT SQUARE BRACKET, <none>
1b    OEM_6        0    005d    005d    -1        // RIGHT SQUARE BRACKET, RIGHT SQUARE BRACKET, <none>
1e    A        1    o    O    -1        // LATIN SMALL LETTER O, LATIN CAPITAL LETTER O, <none>
1f    S        1    i    I    -1        // LATIN SMALL LETTER I, LATIN CAPITAL LETTER I, <none>
20    D        1    e    E    -1        // LATIN SMALL LETTER E, LATIN CAPITAL LETTER E, <none>
21    F        1    a    A    -1        // LATIN SMALL LETTER A, LATIN CAPITAL LETTER A, <none>
22    G        1    y    Y    -1        // LATIN SMALL LETTER Y, LATIN CAPITAL LETTER Y, <none>
23    H        1    d    D    -1        // LATIN SMALL LETTER D, LATIN CAPITAL LETTER D, <none>
24    J        1    h    H    -1        // LATIN SMALL LETTER H, LATIN CAPITAL LETTER H, <none>
25    K        1    t    T    -1        // LATIN SMALL LETTER T, LATIN CAPITAL LETTER T, <none>
26    L        1    n    N    -1        // LATIN SMALL LETTER N, LATIN CAPITAL LETTER N, <none>
27    OEM_1        1    s    S    -1        // LATIN SMALL LETTER S, LATIN CAPITAL LETTER S, <none>
28    OEM_7        1    z    Z    -1        // LATIN SMALL LETTER Z, LATIN CAPITAL LETTER Z, <none>
29    OEM_3        0    0060    0060    -1        // GRAVE ACCENT, GRAVE ACCENT, <none>
2b    OEM_5        0    005c    005c    -1        // REVERSE SOLIDUS, REVERSE SOLIDUS, <none>
2c    Z        0    003b    003b    -1        // SEMICOLON, SEMICOLON, <none>
2d    B        1    x    X    -1        // LATIN SMALL LETTER X, LATIN CAPITAL LETTER X, <none>
2e    C        1    j    J    -1        // LATIN SMALL LETTER J, LATIN CAPITAL LETTER J, <none>
2f    V        0    002e    002e    -1        // FULL STOP, FULL STOP, <none>
30    X        0    002f    002f    -1        // SOLIDUS, SOLIDUS, <none>
31    N        1    b    B    -1        // LATIN SMALL LETTER B, LATIN CAPITAL LETTER B, <none>
32    M        1    m    M    -1        // LATIN SMALL LETTER M, LATIN CAPITAL LETTER M, <none>
33    OEM_COMMA    1    w    W    -1        // LATIN SMALL LETTER W, LATIN CAPITAL LETTER W, <none>
34    OEM_PERIOD    1    v    V    -1        // LATIN SMALL LETTER V, LATIN CAPITAL LETTER V, <none>
35    OEM_2        1    q    Q    -1        // LATIN SMALL LETTER Q, LATIN CAPITAL LETTER Q, <none>
39    SPACE        0    0020    0020    -1        // SPACE, SPACE, <none>
56    OEM_102    0    005c    005c    -1        // REVERSE SOLIDUS, REVERSE SOLIDUS, <none>
53    DECIMAL    0    002e    002e    -1        // FULL STOP, FULL STOP, 
KEYNAME
01    Esc
0e    Backspace
0f    Tab
1c    Enter
1d    Ctrl
2a    Shift
36    "Right Shift"
37    "Num *"
38    Alt
39    Space
3a    "Caps Lock"
3b    F1
3c    F2
3d    F3
3e    F4
3f    F5
40    F6
41    F7
42    F8
43    F9
44    F10
45    Pause
46    "Scroll Lock"
47    "Num 7"
48    "Num 8"
49    "Num 9"
4a    "Num -"
4b    "Num 4"
4c    "Num 5"
4d    "Num 6"
4e    "Num +"
4f    "Num 1"
50    "Num 2"
51    "Num 3"
52    "Num 0"
53    "Num Del"
54    "Sys Req"
57    F11
58    F12
7c    F13
7d    F14
7e    F15
7f    F16
80    F17
81    F18
82    F19
83    F20
84    F21
85    F22
86    F23
87    F24
KEYNAME_EXT
1c    "Num Enter"
1d    "Right Ctrl"
35    "Num /"
37    "Prnt Scrn"
38    "Right Alt"
45    "Num Lock"
46    Break
47    Home
48    Up
49    "Page Up"
4b    Left
4d    Right
4f    End
50    Down
51    "Page Down"
52    Insert
53    Delete
54    <00>
56    Help
5b    "Left Windows"
5c    "Right Windows"
5d    Application
DESCRIPTIONS
0409    Dvomak-En
LANGUAGENAMES
0409    English (United States)
ENDKBD