Jamie, I also did my visa stuff in Ecuador, and we also stayed for a weekend. It's quite a hassle, so it's good not to rush and take your time.
We once went to Ecuador from Tumbes and found that to be a no-go. Tumbes es un hueco and we missed our bus, had to wait for hours to catch another one. From Tumbes, there ar no direct buses, so we first had to take a bus to Aguas Verdes, and from there take a mototaxi to the border, then cross the border on foot. Very annoying and arrived in Ecuador at 05:00am.
So the next time I had to go, we took a direct bus to Guayaquil from Piura (Cifa buses, drive like hell). We installed us there for the weekend and then travelled back to the town where the consulate is (don't remember the name right now). That's a 4 hour drive and quite comfortable.
One funny experience at the consulate (so be prepared):
We arrived on a Friday and were told in Lima that the visa would be done 'al toque'. So we expected to be there for only an hour or so. Then, the clerk told us: "For your visa to be issued, I have to call to Lima first (which wasn't true of course) and asked us to get him two phone cards in town. In the meantime, he'd get my visa ready to take with me. He said: "If I can't make the call to Lima, you only have the visa on Monday." So OK, better get him his phone cards than pay for two more nights in that boring town. When we gave him the cards (and he handed me my visa), I saw him put them in his drawer... full of phone cards! So what he does with them is a mystery to me. But for the rest, the visa hunting in itself is a quickie.
So good luck, Jamie, and while there, enjoy Ecuador. Eat good and cheap, and Guayaquil is a great city, FYI!