I use different tools for different purposes.
Shoutbox archive
You can restart it or load a savegame, after that you'll see the changes you made and saved.
Both minimap AND terrain are generated by the game on the fly from .png file you drew.
Even more often you will make them from scratch. Do major details orientate yourself on, then get to smaller details. It goes somehow like that. No tool nor method is forbidden with reliefs!
You may want to cut parts of already done reliefs and place them on others, rotate them, play with their levels, thus creating new reliefs without picking a brush. This will not be enough though, so, then you will pick a brush and do more editing.
I myself use GIMP. Sometimes I use layers and save images as .xcf that "remembers" layers before exporting into plain .png.
@LRV, ha-ha, creating landscape is a lot of pain for me as well... But if you take the right tool and learn some tricks, it should be very possible for you then.
If you fail to figure out how to setup userlevel creator to use it, look at how it's done in my Returbot mod.
I also very, very strongly recommend you to arm yourself with this: https://colobot.info/forum/showthread.php?tid=723