i am so sorry that it has taken so long for anyone to respond to this post.
Classic99 recognizes the following file extensions as cartridge roms: .C, .D, .G, .3 and .BIN.
to open these files, extract them to the Classic99 folder then open classic99 and go to Cartridge\User\open:
then choose the rom you want to play.
as for the .DSK files, i too am having trouble running these files. as far as i can tell, it seems to be an issue with the way the emulator is made. but i'm not an expert so don't quote me on this.
i hope this helps you some.