@ Lindsey,
just a comment. you say you want to spend time in the smaller less touristy towns, but you afraid if the places are deserted?
travel can be an expensive hobbie for people. Since us in the USA have to spend some (alot?) of $$ just to set foot on soil overthere, that cost can eatup alot of vacation time. Also, we loose 1 full day traveling to there.
Look at:
http://www.skyscanner.com/
http://www.kayak.com/
for some flights costs. Also, the sooner you book the better the prices can be. Note that traveling during "tourist" season can be more expensive. just because you may want to travel "off" season doenst mean you can have fun either. I choose to travel in March or September when its at either the early start or starting end of tourist season. Some drawback is the weather may not be as nice. But im not a sun worshiper so it doesnt affect me as much as people that live by it.
One other hint it to look at flying open jaw- in one city and out of another. ALso, differnt days of the week can make a difference too.
Once you get on land, look at this site.
http://www.seat61.com/
there is alot of info there for using the trains. I like train travel since i hate driving so im really biased, but its really nice to take the trains since they go from city center to city center and you dont have to screw around looking for transportation from the airport to the city.
Also, get some guide books for where you want to go. If you dont know where, then you have a problem and will need to figure that out since you cant plan for it unless you know. There could be some things that you need a reservation for unless you want to spend more $$ to do so. You can also look at your local library for travel books, or if youre lucky your area may have a "travel group meeting".
What i do for ease of travel is to try and plan my travels in some path. i find that bouncing back and forth around eruope can be more expensive and you will loose sight seeing time by doing so. If you can, try to make a linear path or a circular path so that you dont cris-cross your path and waste time.
One last comment. Take a look at Rick Steves, "Europe through the back door". It has some really good tips and is the one i used on my first trip and with several others. I still use the hint/tips since its a tool you will use everytime you travel.
happy trails.