I checked the tutorial file and for some reason, it appears that it did not save the absolutely amazing directions I wrote in it. Hmm. Here's a new version of what I did.
Multiple time signatures within the same song
01. Create Matilde Tracker (MTrk) Generator and link it to the Master Tracker.
02. Go to the Pattern Editor and change the pattern length to 20 (Ctrl + Backspace). Fill in a beat using samples loaded and specified in the Wavetable.
03. Make a new pattern, length 16. Fill in a beat.
04. Go over to the Sequence Editor and change the step to 4, the greatest common factor.
05. Enter the MTrk patterns into the Sequence Editor.
-- Now you have two patterns with different time signatures within the same song. The first one, length 20, is effectively 5/4 since it is 20 ticks @ 4 TPB (ticks-per-beat, controlled by the Master). The second is length 16 and 4/4. A more complex time signature merely requires a different pattern length. The denominator of the timesignature will always be 4 unless you change the TPB value.--
Multiple tempos within the same song
06. In the Sequence Editor, create a new track for Master.
07. Go back to the Pattern Editor and create two new patterns. The length isn't really important if you want to change the tempo at the beginning of a measure, but I made the lengths correspond to the MTrk patterns we created above.
08. Enter in the hexidecimal values for desired tempos in the patterns. In this case I entered 00A0 for 160 bpm and 0078 for 120 bpm. There is a readout in the status bar at the bottom of the screen indicating the decimal value for each hexidecimal entry. If you don't have a hexidecimal calculator, or can't do it in your head, guessing is pretty easy.
09. In the Sequence Editor enter the patterns under the Master track.
-- The tempo will change to whatever you specified in a Master pattern when that pattern is activated in the sequence.--
Multiple instruments with different time signatures
I don't know if it's possible to do multiple instruments at multiple tempos at the same time, but it is very likely.
10. Create another Generator, in this case the FSM Infector (a really good, all-purpose synth) and link it to the Master.
11. Create a pattern for it. I made this one length 12 for 3/4 time.
12. Enter the pattern into the Sequence Editor in the Infector track.
Also note that you can create multiple tracks in the Sequence Editor for each machine.