Now that we have 3 kinds of electronic upgrades (500-milers, regional, SWUs), how am I supposed to choose when I use EasyCheckin to check in?

I just flew SFO-BOS. I must admit that I didn't study the EasyCheckin screen, but it asked me how I wanted to upgrade and I thought I saw one entry for "Electronic Upgrade" and one for "Paper Certificate". I chose "Electronic", and UA deducted 500-milers. Not a big deal, but I probably would have used a regional and kept the 500-milers for shorter hops.