1-2) It's going to be entirely up to you. As long as your material is sorted and stays sorted once it gets to Boardsort, get the material in the box(es) however you can. You'll also want to make sure the shipping cost doesn't cost more than the material you're sending.
I personally fill individual boxes/storage containers up until the box is full or I can combine anything to fill a box.
For instance this is a shipment I sent awhile back.
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File comment: Bottom of box
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I had enough pinless processors to fill the bottom of a large flat rate box. Over that I put a cardboard separator.
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File comment: Middle
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Not pictured in the box but I placed other sorted processors on top of that so they fit pretty tight.
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File comment: Batt/Weights
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Again not a great picture; but on top of everything else I had enough room to send in some batteries; always fun to tetris things in.
Or another box that was just one item, HDD boards:
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File comment: HDD boards single item
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I pack all of this very tight so there's no movement of material inside the box; then I tape the box extremely well; every edge of the box is taped and several wraps all the way around in different locations so that every face is taped at least once. Overboard? Maybe. But no material lost yet.
3) RAM that is manufactured with chips only on one side are still paid for as Gold/Silver/Tin RAM. Blanks are specifically manufactured with no chips. If you have RAM that is missing chips you may or may not get the higher rate depending on how many chips are left.