I made a pcb board and without looking I used pins 49 and 48 on the mega, I did not know those 2 pins where not used/mapped with Arduion. is there any way to add them to the map or refer to them from the Arduino ide? Direct port manipulation will not work, because I need to pass them to a library.
The pin layout is specific to each 'variant' and the boards.txt file specifies which variant to use for each board. In the sketchbook ('Arduino') folder there is a 'hardware' folder. Inside that you create a folder for your board. In that folder you put your boards.txt file and a folder called variants. In that variants folder you put a folder for your board. Inside that you put a pins.h file to do the pin mapping.
Look at the ATtiny support from the High-Low-Tech project at MIT to see how it's done.
I think the file is actually named pins_arduino.h.
There are 3 arrays that you modify.
The first is the list of ports being used.
The 2nd is the specific bits of that port.
The 3rd is whether the bits have a timer associated with them.
There are also some lines earlier in the file that define how many IO there are in total.
Also lines that define the analog/digital numbering - need to check those to make sure the updating of total pins does not impact the analog to digital mapping.