- If you use Publisher to generate building story export modules, you can create 'module export' views for publishing modules with only the layer content you need to send from the building file to the site file, which allows you to place different content on the non-exported layers in the site file and the building file, among other advantages;
- when working on the building files keep all solid element operations (not sure about trim-to-roofs) within the same Archicad story (their elevation doesn't matter; you just want all the elements involved to have the same home story); in the site file, avoid solid element operations between module and local elements, which you will need to redo every time you update modules;
- when generating the story module do not include 'visible elements from other stories' (there is some checkbox somewhere);
- unless absolutely necessary in a given element for whatever reason (rarely the case) keep all walls and openings 'symbolic'; your computer will work noticeably faster, and with sloping terrains and buildings placed on different levels it is usually the only way of getting readable site plans;
- sometimes buildings have mismatching story elevations and heights, so that say the third story in Bldg A will need to show on the same site plan as the fourth story in Bldg B, there will be some funny site basement or mezzanine story showing only some of the buildings, etc.; make sure module names identify the building and story ('BlgdA-01' or whatever), and I recommend including all the matching building story names in the site file story names (such as 1.A02_B03_CB1). When creating the site model, you just place each building story module on the corresponding site story (the Archicad home story will be fine, but the elevation will most likely not) and then elevate the module to its correct elevation and/or move it up or down on the 3D window;
- at some point in the process you will need to create attributes (layers, layer combinations, whatever); from the start decide which site or building or dummy/master file will be your 'attribute management file', and always create/modify stuff there and then update the other files (you can just overwrite everything) using Attribute Manager. Otherwise you end up creating different things with the same attribute ID in different files, and when placing or copy-pasting across files chaos ensues.
[I never link element height to story height for the same reason I try to keep things symbolic. For modules with linked heights there is some option checkbox when importing, so that the module elements don't take up the site file story height. I think, because as I said I avoid all that.]