I use the BX1 boxes on the odd occasion, it's pretty good value and basically the only eBay label I ever purchase (BX box prices are a lot more expensive via C&S - I think the 1kg one is only just under the 3kg satchel price with them 
, but I get discounts on other postage services if I buy from AP directly).
When someone makes separate payments but I combine, I refund excess postage from the lowest-priced item so that I can remain fully covered for seller protection on the highest possible amount, so would do similar for multiple items (if postage was charged).
You are supposed to only use AP's boxes, I think it's part of the deal for getting the discounted postage rate because their boxes aren't too cheap unless you buy a couple of hundred at once (they also tend to be a few grams heavier than others of the same size). I know other sellers have used generic boxes without issue, but I just buy the AP ones.
Sometimes eBay will let you add the same number to multiple items, sometimes they won't, I usually do it via Selling Manager Pro and just use the 'Add tracking number' link from there (I personally find it's more hit and miss if you use the link from the normal selling view, strangely).
eBay labels can only print one to a page, even though they only take up a quarter of a page. You can switch the orientation to landscape to print two if you ever need to do more than one - I use clear document pouches to protect them when I attach them to the boxes, as printed labels are very susceptible to damage (water, etc) - there's some small ones you can get that only just fit a label inside, which are worth looking at if you'll use a lot, but taping down should work well enough too.
