I have only worked on 2-level set once as an SM and once as an ASM.
When I SM'd, we had the TD build a mock-up level of our elevated platforms - not as high, but it helped the actors somewhat understand going up and downstairs and get a feeling for the multiple levels. Not sure if your company has the means to do that, but if they do, it's a big help!
As far as notating blocking, I'm a big person for labeling things with numbers: chairs, tables, entrances, etc. Depending on what is easy for you to understand, you could short hand it with L1 for your first floor and L2 for your second floor. I would label doors with D1, D2, etc. So if someone enters from the first door on the second level:
Joe Ent D1/L2.
Or something like that. It has to make sense to you - and once you find what you're comfortable with, create a key - perhaps just drawing on a reduction of your front elevation, so that someone else could read your blocking later, if need be. For myself, I'll refresh myself at the top of every blocking page with a little ground plan and put in my numbered chairs, entrances (with numbers to match my cue lights at those entrances), etc - so that I don't forget from page to page.
Also - check out our BTDT (link in the top right corner). I'm sure someone has done Noises Off on here and should be able to offer some advice if you message them.
Best of luck!