I just saw this message but thought I'd reply if you were still interested.
I've had flat feet my whole life. Very flat feet. I mean, when I walk out of a pool, it looks like a prehistoric reptile has just walked by and those are its footprints.
My advice, any time you're under load use some type of orthotic. I use orthotics from the "Good Feet" Store. I've actually had many custom ones, and these were the best...by far. The people at the store will fit you.
That being said, I also use minimalist shoes, but ALWAYS use orthotics when under load or when doing plyometric work. I do however encourage barefoot training when warming up and doing mobility work to strengthen your foot muscles. This helped a lot. When you're under load, your flat feet will always tend to collapse at the arch no matter how strong your feet get. Especially with hundreds of pounds on your back.
Also, I have invested in weightlifting shoes, and put my orthotics in these as well. These shoes were a great purchase, and really helps with ankle mobility issues.