Hello all, and sorry for my non-stop questions in advance!

I am looking create a world, which is semi-realistic (in relation to climate areas, etc) and I then want to create a series of maps. I have been messing around with FTpro and it is great so far - however I would like to add more personalisation, probably in photoshop, now I am very new to mapping and PS so bear with me if the questions seem self-explanatory.

Lets say I find a nice world in FTpro and I decide I want to keep it. From this I would be looking to create maps including:

'satellite' type view (doesn't have to be too realistic, just one which shows the desert, ice, etc) and generally looks nice.
altitude map - one with colours for different altitude and one with contour lines
climate map - showing the various climate regions, I would like to do these by hand and not rely on the FTpro generated ones
political borders map and other misc. maps that don't require too much physical things represented

Now, because I want to stylise each map a bit more than FTpro allows (I'm not complaining about this - I realise FTpro is not a graphics editor) what exactly should I keep or discard from FTpro?

For example; if I want to keep the majority of FTpro mountain ranges, but perhaps edit a few myself (outside FTpro) - is it possible to make sure they always appear in the same place on other maps showing altitude? I guess I'm trying to say, is it possible to keep uniformity throughout the maps even though I will be editing them with PS?

I hope my questions make sense...

Thanks everyone!