Are you supposed to layer regular kicks with 808s or should they just be a sepe...

I do both. 808+ kick sounds cool, but it has long tail sub. So you must set polypony to '1'.
When separate i make simple 808 pattern, then layer kicks between them.
 
Layering two types of kick just means they play at the same time. Whether that happens because they are in the same sampler cell or in different patterns or are buss grouped or aren't is generally irrelevant. What matters is how you treat each drum sound (which might require specific routing or whatever depending on your DAW). But DAWs are fairly flexible now so you can pretty much do it however you want. If you want both layers to go through 1 compressor then you need to set it up to allow that to happen. If you want them to be able to go through different EQs then you have to set it up to allow that.

What's more important, when layering kick drums, is to understand phase relationships.
 
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