Or alternately you can just use CE's Modfolder feature and put the retail levels in one folder and the beta once in the other, then simply edit the tp_mod.ini file to swap out the different versions as if they were mods. Works extremely efficiently! Unless you want to actually use the different engines, then you'll want to do what machf suggested.How to use modfolders:
1. Create a folder called "Mods" in your Tres directory (where the .exe file is located).
2. Inside of this new folder, create folders for all of the different mods you want to install. You should preferably use short names for the folders (ex. JPDS, TCT, B116) when doing this to make it easier when switching.
3. Create an .ini file in each of the mod folders named "fm.ini". Paste this into said file:
These settings define TPA files that will be used alongside the normal Effects, Stream and Ambients TPAs. The StartLevel is the level that will be loaded when you hit "New Game" in the menu, so for the original game this would be "BE.scn". You should change these to be appropriate to each mod loaded, or simply make them blank if no extra TPAs are to be used. Make sure you include the .scn extension for the StartLevel and the .tpa extension for any extra TPAs.
4. Install the mods you want to use to the appropriate folders that you've created. All you need to install from each mod is the "Data" folder as ATX-related stuff such as modified EXEs or the MAPS folder are not used in CE (unless you want to use those independently of CE).
5. Go back to your main Tres directory and create a new .ini file called "tp_mod.ini". Paste this in:
;Change this to the name of the mod folder that you would like to play.
Now, to change the currently active mod, you simply have to input the name of the modfolder that holds the mod you want to play after the "ActiveFM=" line. So if JPDS is installed to a folder called "JPDS", you will put down "ActiveFM=JPDS".
6. Start the game via the regular CE executable and see if your mod is working! You can change the ActiveFM to another mod if you want to play something different. This will allow you do play the different versions of the original game or swap mods without having a bunch of different installs or having to mod the registry. The only setback of using CE is the few missing ATX actions, so if a mod REALLY needs ATX (they all appear to work fine on CE but are missing a couple of features - specifically, JPDS is missing cutscenes and East Dock is missing rain and the spitting dilophosaurus), you shoul;d use ATX instead.
Hope that clears up the use of CE's modfolders so that this feature becomes a bit more popular as I feel that at the moment it isn't quite as popular as it should be.