1.) look for recipes that indicate their stats, and efficiency. Ultimately that drives the scaling accuracy... So if the recipe expects 60%, and you average 75%, you adjust for that. Personally, I would just attempt to match gravity, ibu and color as I transcribe into the program for my volume/efficiency - good practice to learn extract potential. Otherwise, you use the scaling tool, adjust for your efficiency and then manually tweak the weights and volumes of ingredients.
2.) this issue is more about mash pH. You could acidify your sparge water such that the mash pH doesn't exceed an arbitrary level, say 6.0. Bru'n Water can help you calculate. Also make sure Beer Smith is using your actual hourly boil off, and not the percentage. That used to throw volume errors, but it may fixed in the latest version. If you are sparging with RO, you are probably fine with the acid.
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