Separate boxes for hygiene products and snacks is absolutely recommended. In the event that the box sits for three weeks in 110-degree heat you don't want the cookies to taste like the soap. The only exception to that is packages of razors or anything that isn't chemically-based, if you don't have other hygiene products going at that moment.
There are other boxes at the post office that are free. Ask for Priority Box #7 which is 12x12x8 inches. That's my favorite one for toiletries. For snacks I like the 12x12x18 ones I buy at Staples. They're sold at 3 for 11.95.
I stopped using the flat-rate boxes when I discovered that I wasn't saving any money. This morning I sent three #7 boxes, total weight about 62 pounds, for $37 total postage. Flat rate boxes are meant for ebay sellers for the ease of calculating postage, but they are unlikely to hold enough heavy supplies to make it cost-effective for me. Check the postal rates from your area: Unless you pay more than a dollar a pound the flat-rate boxes aren't worth it.
Finally, anything you send to a person found through AnySoldier.com is shared. Many soldiers who receive stuff from family share it, too.