Actually, there aren't that many time zones in Central Europe. Most likely you won't be crossing multiple time zones that often.
If you first import each time zone into a separate project, and then follow the instructions here, you should be fine. Any constant offset between photo time stamps and GPS time stamps is fine – indeed, Aperture basically assumes that there is some offset.
No matter what you do, it will be a lot of manual work. Matching GPS tracks and camera timestamps is not that straightforward (camera clock drift; GPS errors; indoor locations), and the somewhat unfriendly user interface in Aperture does not help.
If at all possible, I would try to do geotagging as soon as possible. If you are going to have a laptop with you, you might prefer to geotag daily. That way it will be easier to remember what you did.
It might be a very good idea to take a "calibration shot" each day. For instance, while walking with your GPS on, take a sharp turn and shoot a photo quickly (don't stop). Then it'll be easy to drag'n'drop this photo in the right location along the track (remember that the precise geographic location is not significant for this photo; it is the time dimension that matters), and Aperture takes care of everything else based on the timestamp offset.