"If I'm layering kicks or snares should the waveforms be pointing up or down together and at the same time?"

It's hard to say that matching the kick and snare matters without looking at a specific situation. It's routine to check both ways when working with a acoustic kits and a multi mic setup to decide what sounds better.

What probably matters more when layering drum tones is that both sources of any single "instrument" are matched.

best regards,
mike

I agree..... if it sounds good to you, I would not sweat the phase issues. 

Many folks switch to mono to check for major phase issues..... In stereo, things tend to work OK. 

I love looking at waveforms. And I love watching meters. But I would only ever judge phase or polarity issues by ear. Waveforms and phase meters don't actually tell you if there's a problem or not. They might clue you in that there might be a problem and lead you to do a sum-to-mono phase check, but the final call is the listening test. Your waveform and meter might show radically out-of-phase signals, but on listening to the stereo and mono mix you might not hear any problems.