It's a while since I used FCE because everything I do is in FCP nowadays. The last FCE version I had was (I think) 3.5, so take what I say about FCE4 with a pinch of salt. I can tell you how it is in FCP, but assuming FCE4 was a superset of FCE3.5 and a subset of FCP you should be OK.
Shooting in AVCHD requires you to use the Log & Transfer dialog. In that dialog you can generally preview the footage and set in/out points if you don't want the entire clip. Alternatively select everything and import it all
. Once it's been transferred you are ready to edit. Note that if you want to backup the footage from the card (actually the PRIVATE folder and everything within it) before importing it to FCE then you need to copy the entire card to a folder on your hard disk because FCE uses the entire folder structure to validate the footage prior to import. If you didn't copy the entire card then FCE will refuse to import and you will need to find a third party tool to transcode for you (e.g. Toast 10).Shooting in MJPEG is a little different. Unlike AVCHD, the footage shot in MJPEG is not placed in the PRIVATE folder on the card, but is instead placed in the DCIM folder along with the stills. In this case you can drag the .mov files directly to your hard disk and start editing. There are advantages and disadvantages to both methods. The advantage of shooting MJPEG is that you don't have to go through the Log & Transfer process, but the files are quite a bit larger in the first place.
I am also in PAL. I usually Log & Transfer to ProRes 422, but I don't think you have that in FCE4 (I could be wrong), so you will probably be using AIC (Apple Intermediate Codec), which is still generally very good, but the files are a little larger (in terms of MB) than ProRes.
If you are always going to be shooting in the same mode (1080 vs 720) then by all means set up your preferences to always be in a mode that matches. I don't always have that luxury, so I set mine up on-the-fly as needed.
Create a sequence that matches the footage, so if you shoot in 1920x1080 @ 25p then create a sequence that is 1920x1080 @ 25p. If you are shooting at 50i then create a sequence that is 50i. If you are shooting 1280x720 @ 50p then your sequence should be 1280x720 @ 50p. Simples
I can't remember if FCE does this or not, but I normally create a new sequence in FCP and don't worry about what the settings are, because when I drop the first clip on to the sequence in FCP it automatically warns me if the sequence and clips don't match and asks if I want to change the sequence to match the clip (answer = yes). With this in mind I normally don't need to manually set sequences or touch the preferences at all.
In terms of viewing yourself, it depends on the device you are viewing on, and how you are editing. If your screen is at least 1920x1080 then by all means shoot and view in 1080. Don't sit too close or you will notice artifacts! If you are looking for action shots or the ability to slow footage down during editing then shoot in 720/50p. This is by far my most used mode, but then I'm not trying to be the next cinematic hot shot. Others prefer to shoot 1080/24p because they are trying to target 'the cinematic look' more. In this case you will need to check how the Log & Transfer window is handling things. FCP removes pull-down automatically. I'm not sure what FCE4 does.
I normally upload to Vimeo using an H264 codec @ 1280x720 25p. This does two things. Transcoding from 50p to 25p halves the file size I am uploading and converting to H264 makes it much smaller too (typically 10% of the original size) without much loss in quality. I do notice a small colour shift when I do this, but only when you view the footage side by side. Most people would never notice it. I typically leave the keyframes set to 25 but this is something you can experiment with based on the action in your footage.