Is it bad to use unmatched tubes? For example, if one of my JJ KT-88's went, could I throw in a EH KT-88 to get me by until I get more, basically is it a big no-no or does it just affect optimum performance?
You should use pairs of tubes that are about the same strength. Depending on how the amp is biased (individually or in pairs) putting a new tube with a weaker one can put extra stress on the weaker tube, so replacing pairs is the way to go.
Also I see tubes being sold in matched pairs/sets. How important is this? If I use 4 output tubes, I'm assuming it's 2 per channel. For the best results would I want 4 matched tubes or is 2 pairs of matched tubes fine?
2 pairs should be fine (yes, 2 per channel). If the tubes were all produced at the same time, they should be pretty closely matched as is, but for a few extra bucks, it's no big deal to get matched ones.