FILE "C:\SEGA\SEGACD\MORTAL KOMBAT (USA)(BIN-CUE)\MORTALKOMBATU.BIN" BINARY
your cue references a direct path that is not where your bin is. should beFILE "mortalkombatu.bin" BINARY
don't know about the second one. does the bin/cue launch when you run it in the emulator as is? what is the error message that CHDMAN gives?