Little circles are potency upgrade, yeah. When you get a 6* and beat quest #200, there's another icon that appears on 6* medals called guilt that gives a straight damage bonus. That guilt bonus is essentially a 6th circle on the 6* card so you need a 6* card with 2 filled circles and a 6* card with 3 filled circles to be able to combine them both to get guilt bonus. The 600 jewel pull is 150% more efficient at getting more medals than the 3000 jewel pull so right now it's the best. I assume in the future there might be a very lucrative 3000 jewel pull that would give you better odds at getting the best medals, but right now the medal pool isn't very big so that's certainly the best option.
Here's something that'l help for farming the common medals: https://docs.google.com/spreadsheets...sle=true#gid=0