The thing to enter is a 'Name' from the Codes page of the docs, so for the shifts...
unstrobed -PD1 LSHIFT
unstrobed -PD2 RSHIFT
The matrix position is worked out from the code such that 00 is top-left, increasing along the first row until 07. Then the second row is from 08 to 0F. Then the 3rd and fourth rows are codes beginning with 1, and so on.
Again, just put a name in each position of the matrix. Many are obvious, so you won't even need to look them up in the Codes list, e.g. A, B, C,... 1, 2, 3, ... F1, F2, F3, ...
So if you found that 00=A, 01=B, 02=C, ..., 07=H, then you would enter them in like this:
sense PB0 PB1 PB2 PB3 PB4 PB5 PB6 PB7
strobe PD7 A B C D E F G H
To give another example, this is the config I made for my mini keyboard:
led caps -PC6
led scroll -PC7
matrix
scanrate 1
debounce 5
sense PB0 PB1 PB2 PB3 PD0 PD1 PD2 PD3
strobe PF0 ESC 2 4 5 7 9 MINUS LCTRL
strobe PF1 1 3 UNASSIGNED 6 8 0 BACKSPACE LGUI
strobe PF4 TAB W R T U O LEFT_BRACE LALT
strobe PF5 Q E BACKSPACE Y I P RIGHT_BRACE UNASSIGNED
strobe PF6 CAPS_LOCK S F G J L ENTER RALT
strobe PF7 A D SPACE H K SEMICOLON UNASSIGNED MENU
strobe PB6 LSHIFT Z C V N COMMA FN2 RCTRL
strobe PB7 FN1 X UNASSIGNED B M PERIOD RSHIFT UNASSIGNED
end