i am assuming that you will be using JSGME to apply not only TMO but your changes as well. if that assumption is incorrect then now is the time to say so.
ok.
unzip TMO into the MODS folder.
then create your own mod folder with a different name under MODS.
you will want to copy the files that you wish to modify into your mod folder.
then edit each of the files on your list in the MODS folder. .CFG, .MIS .UPC should be edited with a straight text editor like Notepad. .SIM, .ZON, .DAT require skwas' S3ditor.
when you are finished making changes then apply your mod after all of the TMO mods.
i've created an example for you.
ignore the mods on the left.
Notice the last mod in the right panel (TMO RSRD Tweeks)? that would be where your personal mod should be.
so, now, when you encounter a problem or you wish to make additional changes, run JSGME and remove your mod, make your changes, then run JSGME to apply your modded changes.
good luck.
