Lets say I have IMP and medium both with virus counters on them. I do a successful run on R&D. They have an upgrade on that server. Do I access the cards in R&D first or the upgrade?

From the rulebook:

"When accessing multiple cards, the Runner accesses them one at a time in any order he likes. For example, the Runner may access a card from HQ, then an upgrade installed in the root of HQ, and then another card from HQ, if he has the ability to do so."

So it's up to you which to access first cards from R&D or upgrades.