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An alternative to using BrickLink for those purposes would be http://rebrickable.com. I personally find the interface to have some warts, but definitely better than BrickLink in a lot of ways. In particular to your requested features it does support importing parts from sets (Look for the "Add to my Parts (Part out set)" link on any set description page) as ...
We have a small business sorting LEGO for customers (www.brick-sort.com)... and we've tried many different machines. Bottom line is that, unless you're dealing in tens of thousands of parts, Pubby is right: "...the time it takes you to build and use one of these is probably greater than the amount of time it takes to sort by hand." I think people forget ...
A lot of people prefer wide, shallow boxes to store parts — because it allows you more surface area to see what's in there. A Dollar store is a great place to get cheap storage containers.
The easiest way to achive what you want to is register as a seller. You don't have to sell anything (you could keep your store open but empty, or you could just keep your store closed). Once you have a seller account you can manage two stockrooms: A and B. If you do have some sets/parts you are planning to sell and want to have an active store, you can ...
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