I got used to using WaveLab on a friend's PC for stereo mastering, but now I'm attempting to use Cubase SE. The problem is, if I'm trying to eq only a section of audio (i.e., one or two tracks in a dj mix), I don't really see any way to apply a VST eq and process just that one section.

I'm using Cubase SX but guess it'd work the same.
If you want to use a VST effect on just one section, try using automation.
If you turn on read/write for that vst and move the 'wet' effect slider/knob, cubase should create an automation line for that parameter. Just set the ramp to 100% where you want it, and 0% where you don't.
TaDa!

I don't use Cubase, but I'm prepared to bet money that there's a Master Bypass on plug-ins that can be automated.