It depends a little on your current mod and credit situation.
Right now I focus mostly on slicing mods. I had a huge number of mods with speed secondaries, and I've been slicing only those. As I get new mods, I level them up enough to see their secondaries. If they have speed, I'll level them to 12. If no speed, I sell them. Then I slice the mods with speed secondaries, focusing on the ones with the highest potential (so the blues that have upgraded speed twice, the purples that have upgrade thrice, etc). Then I periodically switch over and slice a gold mod up to 6E.
Eventually I'll run out of good slicing targets, and my mod energy will go towards farming new mods from battles. But I get most of my mods from the store at this point, so I can ensure that all my mods have a speed secondary.
