From Vatican area you can take a bus (near Lepanto metro station) directly to the airport. By bus you can also go from Civittavechia to Rome. Not far from Civitaavechia there are very interesting Etruscan sites.

In Prague I'd recommend you not expensive but very nice Pansion Brezina - they have a bit more expensive central quarters near Vaclav square, but I liked more there dependency near the National Theater and Laterna Magica (don't miss Laterna Magica's show!!!!).

Sincerely, Alex Jerusalem Israel