I would concur with those suggesting that you use tack welds to keep everything square before final welding.
Case in point.
I am currently building a ramp door for a trailer out of 2x2x1/8 square tubing, "that size of tubing sound familar to anyone?" It is a 6'x8' door. I made sure my butt angles were straight and tack welded everything together. Measuring diagonally across the door I was about a 1/4 inch off even though I was tacking rather than laying down a bead.
Point is, you can be careful and still be off a little. No biggie, a long pipe clamp moved things back into square and I was able to weld my gussets into the corner and Viola! nice and square once again. It would have been very hard to do that had I went ahead and welded everything.
As far as the double shielding of flux core wire and gas, pick one and go with it. Personally I would always choose gas over flux. And a good anti spatter spray if you don't want to knock off spatter all day.