I think there is some confusion here. I note you say above there are a/c folders, but the a/c cannot be selected. When CFS 2 installs, it creats a lot of different aircraft folders, but doesn't actually put anything in the folders - it's a quirk of the install. If these folders have no contents, the aircraft will not appear in the a/c selection screen. I think this is what you are seeing.
Now, what Rami is talking about is also true - you should look for better CFS 2 native a/c models. Once you've downloaded them & installed them in your a/c folder, they will appear in Morten's utility for selection, & you will be able to replace a/c in any of the missions without opening Mission Builder. (You can also replace ships as well)
There are a few caveats - back up the original missions, or rename the ones you're swapping a/c in BEFORE you swap. Mortens utility doesn't rename missions. In doing so, remember each mission has a .mis file & a .dyn file - change the name of both files, otherwise the mission won't work properly.
Also, remember you are just replacing the aircraft callout - so all the waypoints & speeds & loadouts will match the original mission a/c. This can sometimes give unexpected results, so it's not a perfect solution, but it's a quick way to get a new mission template you can tweak yourself in mission builder if need be.
Hope this helps.