Not to be an annoyance, but the use of the top down terms used is not entirely correct. You are really referring to the organizational hierarchy of your assembly, not the methodology by which it was designed.
Top down design is a method of design that designs parts around existing parts. An example of this is a house who's roof is designed first, after which the walls etc are designed.The roof drives the shape of ther house.This method is typical in some shops where the customer supplies the part, and you design the fixture.
Bottom up design is the more "traditional" method, which as it implies, designs an assembly starting from the bottom up. Using the house as an example, the foundation is first designed, the shape of the roof is dictated by the shape of the walls.
As far as smart fasteners go, I usually just add 1 bolt/feature, to make sure that I've selected the correct fastener and stack up. After that, I just enetr the number manually into the BOM. I find that fasteners in large numbers are visually pleasing, but really take up alot of memory.
regards
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Can't Fix Stupid