Hi kskelley40, and congratulations on deciding to book a cruise in Europe!
First things first -- itinerary. What time of year are you going? For example, the Med is typically very hot in the summer. Do you want scenery, historic sites, a lot of touring? Are you willing to take long bus or train rides to visit major cities? Where would you prefer to embark and disembark... and would you rather do a round trip or start and end in two different cities? Also, what is the length of cruise you're considering?
We've cruised Europe twice... Norwegian Fjords on Celebrity Century in 2007 and British Isles on HAL Prinsendam in 2009, and are booked on a third for this coming April. (By no means does that make me an expert, but I am happy to share experiences.) For all three, we booked our own airfare, mainly to get the flight arrangements we wanted. For HAL, we booked the hotel through them as it was convenient and not much more expensive than doing it on our own once transfers were considered.
But, I'd suggest narrowing down some itinerary ideas first.