Nice job! Keep it up. The more you do it the better and easier it will get. This may have been covered but, what welder are you using? and what size wire? Gas? Ideally a 220 volt welder, but 110volt will work fine. Most welders have a cheat sheet for setup on the inside cover. The chart will tell you wire speed, and heat range for the size wire and thickness of metal your welding. They are usually very accurate. For doing sheet metal I usually use .024 solid wire with argon/co2 75/25 mix.
The patch you made looks good, but could be tighter. I personally like as small of gap as possible. The tighter the better. Also a lot of the issues your having with the weld messing up could be from contamination from underneath. You need to have both sides of the area your welding nice and clean. That patch should of been able to be done with 1 round of the welder and 1 round of grinding. But that will come with more practice. Some of your welds look a little too small. The ones that look good in 2nd pic, look like you held the bead for a second or so longer giving it a chance to form a nice weld puddle. Like cuda said, it does help to have a copper backing plate if you have some holes or gaps and don't want to blow threw.
Another helpful hint when your doing your butt welds is to try to always start your weld on the new piece of metal. The new metal can usually take more heat than the old stuff your trying to weld to. So you want to start the weld on the new piece and make "U" type movement whipping the puddle onto the old metal getting them to bond together. Then you should move and tie next "U" into the first moving in the direction of the open end of the "U". By using this method you have less chance of burning through and less likely that the backside of your patch will look like a porcupine.
Just kidding!! Your doing fine. Takes a lot of practice to get your groove. If you have any more question just ask and keep the pics coming.
Also, for the new floor pan being black. The coating is EPD. A very tuff coating that is applied with an electrical charge of sorts. You will have to grind that off anywhere you are going to weld. When you are done and want to epoxy prime the pans, you can wipe it all down with wax and grease remover then scuff it with a red scotch brite pad, blow it off, wipe again with wax and grease remover, then shoot the epoxy primer.
EDIT: Just a heads up. The u shape technique is good for when you have a gap to fill. Otherwise, if the patch is nice and tight you can just start your spotweld on the new metal and just touch into the old. No need to really move your weld puddle around too much. Also when doing your rosette welds, try not to start in the middle of the rosette. A lot of people start right in the middle and just let the puddle fill up the hole. This will work, but it tends to hump up more in the center and causes a lot more grinding to be done. I usually start on the outside perimeter of the hole and weld in a circular motion. The weld tends to lay down much nicer this way with a lot less grinding.