Using the T48 (Flash Boards)
The only thing you have to worry about when programming to these chips is that you are programming with the correct endianness. Genesis is big endian. What this means isn't super important, but when you're about to program your chip(s), you need to make sure you're programming them as big endian. An easy way to tell this is by looking at the ASCII data at the top of the ROM - if it says "ESAGG NESESI" instead of "SEGA GENESIS" (or "ESAGM GE ARDVI E" instead of "SEGA MEGA DRIVE") then you've got it correct. If not, then you will need to byte swap your ROM.
An easy way to do this is with the GQ-4x4 software, click the "A<>B" button at the top.
Be sure to save this ROM file (if you need to swap the bytes) to a new file.
If your game is larger than 2 MB, the size of one M29F160 chip, then you'll need to split your ROM file so you can program each half onto a separate M29F160. Use the free file splitter tool at Romhacking.net for this. It's very easy to use - just select your ROM file, select the folder you want it to be saved in, and set the file size for 2 MB.
Programming M29F160 chips with the standalone T48 programmer is pretty straightforward. You will need the TSOP48 adapter to program, though. Just place the chip in the adapter, load the ROM file in the programming software, and flash the chip.
Be sure you have selected the proper chip in the Select IC drop down menu.
Remember to mark your chips if you need multiple ones, i.e. two chips for a 4 MB game. Don't mix the order up! U1 will have the first half of the game, U2 will have the second half.