ToBEx installation is handled automatically by SCS(II). You don't need to install ToBEx separately. (If you already have an up-to-date version of ToBEx installed, SCS(II) will just skip installing it.)
In other words, if you don't even know what ToBEx is, don't worry about it. You don't need to do anything, it all gets dealt with behind the scenes.
If for some reason you don't want to have SCSII make use of ToBEx, edit scs/scs.ini or scsii/scsii.ini (as appropriate) and add this line:
SCS(II) will then attempt to do some backup hacking of the BGMAIN.EXE file to make up for the lack of ToBEx. If you don't want that either, add this line:
Nothing catastrophic will happen if you don't use ToBEx (or the hacks), but some features of the mod will work less smoothly. (Dispel Magic will be too effective; Mirror Image will provide protection from area-effect magic; antimagic spells will only imperfectly target invisible creatures; mages' concentration will be slightly too easy to disrupt.)