If you are using the same type of EPROM eg 27C256 for both PRG and CHR, you can make the CHR fill all 32Kb by duplicating it 8 times, then you are guaranteed that the NES is looking at the right CHR data regardless of what the high-address bits are doing.
Filling with FF's means the fuses are not blown, so you can write over that portion without having to first erase the chip. On many processors the NOP instuction had opcode "FF" so you could have "spare" sections of code for bugfixes, esp. when people often used burn-once ROMS.
Also, remember to set your mirroring correctly on the PCB.