It only screws up the editors because of a flaw in the menu.txt and/or game.txt that came with it. There is a fix on these forums somewhere...
This thread, I think:
http://apolyton.net/forums/showthrea...threadid=22735
In any case, the text files are not necessary to make the no-limits patch work. I believe the only differences are that the civ2 version number is changed ("no-limits" added, or so), and the map menu says maps can be up to 32767.
If you still have problems, restore the old text files. You'd still have the no-limits (even though the version won't say so), and you can still make gigamaps (even though the menu doesn't think so).
Still, it IS wise to have both installed (that is, "vanilla" MGE and no-limits MGE), but you can do that simply by renaming one of the executables. Just like people with the CiC and FW add-ons will have civ2.exe (FW), civ2scen.exe (CiC) and civ2orig.exe (2.42, if they patched it, that is), and can still run all of them too.