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To add a new variant to Fairy-Max, you would have to edit the fmax.ini file. This file is self-documentng: it contains a description of the formt you should use. Bascally this is the name of the variant, the initial array of pieces on the back ranks, (not very important, as you can always start from an arbitrary setup position by loading it at the beginning of the game), and a list of piece descriptions. Each piece description consists of a line starting with the letter used to indicate the piece (in promotion moves) and its value in centiPawn, followed by a list of (step-vector, move-rights) pairs for each direction the piece moves in.

To use a newly defined variant in WinBoard, it would have to have a name WinBoard recognizes. WinBoard is not yet configurable for variant rules. But it provides a catchall variant name 'fairy', so you could simply call your new variant 'fairy'. If it contains pieces that are not pre-programmed in WinBoard, you could still play it with legality testing off. Even with legality testng on, WinBoard supports a few piece types for which it accepts any move.

What you cannot do is use pieces whose moves have side effects. (e.g. mat's catapult pieces, Ultima pieces that do use other capture modes than replacement captures, etc.) Fairy-Max is not made for that type of variants. It only served the more limited purpose of evaluating conventionl Chess pieces with deviating move patterns.

What variant did you have in mind?