I wouldn't call this a guide, as much as protips from an expert
A few notes: do some clarification on 'flow'. The people that get it, GET IT, but the people that don't... well... yeah. It's hard to articulate; while I could, I'm too lazy, and you'd do a much better job.
Also, I'd like to think there's multiple forms of layering. The layering you described is what I would call simple layering. Each arrow clearly goes to a distinguishable sound, and there's no confusion when you look at it in the editor (think Ossa, he's the best at this imo). The challenge here is you must be incredibly calculating when it comes to your patterns and occurrences in sounds- otherwise, you'll end up breaking/compromising the 'rules' of your layering, and it ends up being a mess.
The other form of layering, I'd like to think is much more harmonious. This is where you make patterns that are trying to encompass multiple sounds without actually individually stepping each one. Hence, you'll get patterns that are somewhat ambiguous as to what is actually being stepped, because it can be interpreted multiple ways. You need to be very aware of how the patterns look, feel, and interact. (sorry, this is somewhat hard for me to explain, hopefully you see what I'm getting at... if not, I can try to find some examples)
Oh, you might wanna cross post this at ODI, although it might just get shotdown as 'lol stepmania theory'. You're pretty respected in the community though so who knows =P