you need to brush the bits of blue paper towel off before you start welding. A solvent wipe is insufficient to clean aluminum for welding. Use a small stainless brush and brush off the oxide layer. 6xxx extrusions are the worst when it comes to brushing the oxide layer off. As you brush, you will feel the brush bite into the metal instead of just slide across. Once you know what to look for, you will be able to see the surface transition from unbrushed oxide, to brushed oxide, to brushed bare metal. You kinda have to brush the s**t out of it with 6xxx tubes. Try 10 seconds of brushing per side (four sides of tube) to start. Resist the urge to just hammer on it with a power brush, as that will just shove the oxide into the base metal. Brushing in the same direction helps a lot too. Keep your AC balance somewhere around 55% EN to start (around 6-ish on the dial for transformer machines), and move more toward a balanced arc if you still can't get the tack to wet out quickly.
Also, autogenous welds are impossible with 6xxx aluminum. I love 5356 myself, and usually when I get tacks breaking it's because I didn't get it enough penetration. Nearly all extrusions (tubes) are 6xxx, and there needs to be a certain amount of dilution of the base metal with silicon (4043) or magnesium (5356) to prevent the hot short cracking that 6xxx alloys are susceptible to.
When welding 3003, it tacks up just great with no filler, provided your fit up is snug.
You asked about waiting for the two puddles to join. Sometimes they will, but the surface tension is pretty strong, and mostly they will just pull further apart from each other. It's a real problem sometimes getting the arc to evenly heat both pieces when the fit up has even a sub-millimeter gap. I feel like a snake-charmer sometimes trying to get the arc to evenly heat both sides, so what I do is let the arc heat the side it wants to, let the puddle form, then stab the filler in there and use the filler as a thermal bridge to conduct the heat to the other side.
If your fitup is dead nuts snug, the puddle will bridge the (nonexistent) gap and the puddle will flow just fine, but mostly you have to deal with some amount of gap.
Read all you can on Alcotec's website
http://www.alcotec.com/us/en/education/knowledge/qa/How-to-Avoid-Cracking-in-Aluminum-Alloys.cfm