Yep, but you'll have to install AviSynth first.
And you'll have to properly install and ReadAVS for TmpgEnc to be able to read avs scripts since it can't natively do that.
Also you'll have to install any
external filters needed in your script.
So search for the latest stable Avisynth 2.5.5. Use google

.
Install it on a short path i.e. "c:\video\avisynth".
Then search for "readavs" inside the forum.
Download it and make sure you read it's instructions very well.
Install it according to the instructions.
Now it all depends on what script FitCD came up with.
But odds are you won't need any external filters for your movie from the automatically generated FitCD script.
Now load the script in TmpgEnc and voilá.
Hope it helped.
Cheers