I bought GSX at just flight. Can I download it from you side and use my code?
As far as I know, the email from Justflight contained just a link to our site (at least, this is what they are supposed to do according to our instructions, and this is what they confirmed they do, when I inquired about it) so, strictly speaking, you never downloaded anything from them...
Yes, of course you can use your existing Serial Number, but you don't have to use it *now*, just for a reinstall. The only time you will need to input your Serial Number, is when you are updating your hardware, or you reinstall Windows.
Can I overinstall or do I have to deinstall the old version?
We haven't included anything about this in the release notes or anywhere else in our site/forum so, you can safely assume it doesn't matter.
If it was required to uninstall first, we would clearly advised to do so or, more likely, we would have the installer either issue a warning, or perform the uninstaller for you.
Are my saved planes still there with the new version? (Depends on question 2)
Your personal settings are never removed, regardless if you uninstall GSX or not so, unless you manually remove your customized GSX settings folder, they will always stay there.