SI Drum Kit has an error, then disappears.

"And Lo and Behold, there in the options was a tempo-based [Effect] ...option." 

That one word,'effect", is pretty important.
I've been trying to replicate your scenario, but only have partial success.
What I have seen is that checking Configure as tempo based effect moves SI Drums from the VST Instruments category to the Vst Audio Effects category.
However, I can still insert it as a synth. I have not rescanned, which may be a factor.
For whatever reason, I have not triggered the problem, but I can see where it is ready to occur.
Note that Configure as synth/Configure as tempo based effect are radio buttons. Clicking one toggles the other off.
SI Drums is, in fact, a synth, and should be configured as such.
I don't know why the SI Bass would be affected, but double check it as well.

A tempo based effect would be something like a delay that gets its timing from the project tempo, or a flanger that syncs to tempo.

Once Sonar reads the SI plug-ins as synths, that should take care of the error problem.

Now, back to what you were trying to do in the first place.
The SI interface is self contained, but is synced with your project BPM. You can play with the various patterns, but they will not be integrated into your project.
For that to happen, you need to drag a pattern from the SI GUI to your MIDI source track.
These are groove clips (loops), so if you want to repeat them, just grab the right edge and drag them out.
Think of the SI GUi as an auditioning space befor you commit the patterns to your project.
Hope that helps.