If you want to install FSX disk edition to your E drive, first create a folder for it on the E drive.
You can give it any name you like, "FSX" is always good.
Then, when you run the installer, select the custom option and point the installer to E:\FSX.
As you have already been advised, FSX and FSX SE use the same folders if each is installed
alone and if FSX is installed after FSX-SE is already there.
They can be managed like this but it would probably be simpler to uninstall FSX-SE first and
run something like CCleaner to remove its registry entries.
Then install FSX disk edition and if you really need FSX-SE as well, install that.
If you do it that way, FSX-SE will use different folders and each can be used entirely separately.