Brandon, Greg's giving you some good advice.
Let me add my POV. First... on this page>>>
http://www.herbhartley.com/hh2_edited_slimmer_005.htm I wrote out some things to help folks get a grasp on TTS. It can be a bit confusing but once you understand it, you will see it's really pretty simple.
1. Assign the instrument patches inside TTS channels not in the DAW tracks. That will solve this issue of patches changing back on you.
2. The DAW tracks and the TTS channels do not need to line up numerically.... it can be done, but it's not necessary. Tracks in the DAW....Channels in TTS. In my explanation on my website...yes, I did have them aligned.... to do that start on DAW track one and TTS channel 1. Other than that, as long as the DAW track send it's data to the TTS synth channel for the proper instrument patch, that's really all that matters. If you have to have numerical alignment.... put the Synth in audio track #17 in the DAW. That way, Track 1 can be lined up with Channel 1 and so on up to 16 in both.
3. Dropping notes. I have had this happen a few times and mostly when I go back to edit a wrong note I played in with a midi keyboard. I don't know how much you understand about midi so bear with me if you know this already.
Every midi note is actually data and contains a number of note parameters. Pitch, velocity, volume, on time and off time. So each note has a specific on time and an off time. And it's linear. So, if you have 2 notes that are close to each other and due to a sloppy edit or if you are mousing them in..... there is a distinct possibility that you can overlap them.... When you do, and if they are the SAME note.... the sequencer sends the ON signal and the note sounds..... time line moves forward at the tempo..... the overlapped note sends it's ON signal and then very quickly, the first note's OFF signal shuts it off. On the staff view, it looks like the second note is clearly behind the first.... but in the sequencer, it's overlapped and the on signal for it has already occurred while the first one was on.... so it appears that the second note never sounds.... This may or may not be what's going on, but I know for a fact this has happened to me on a number of occasions. The solution is to simply edit either note so that there is no overlap and you will clearly hear both notes sound.
I hope this helps you a bit.
TTS is a very capable synth and is amazing