Start your puddle on the base and let it build to consume the top. Keeping your gaps TIGHT helps a bunch too.
Set your heat and wire speed on some scrap that's close to the same gauge as your welding. Make sure it's as clean as possible, don't grind out to much metal, but don't try to go over rust, paint, grease etc.
Go small, not much more than a series of tacks, and jump around to let the metal cool. If somethings not right, STOP, fix it.
I started doing my floors with .035 flux core, but had much better luck using .030 with shielding gas.