Can I use applications installed on HDD after booting from new SSD?

Hi! I am a little uninformed and require some MacKnowledge.
Relevant hard/software:
MacBook Pro 17" early '11. Lots of RAM. Slow but large HDD (5400rpm, 750Gb, I think.)
OS 10.7.4
128 Wintec Expresscard SSD.
I recently aquired a 128Gb ExpressCard34 SSD and installed 10.7.4 on it just to see how it "felt."
Wow*.
Now I want to boot on that drive exclusively, but have no idea the best way to migrate over my applications.
I could reinstall all applications fresh (as a 20yr PC vet, this is my natural inclination,) but I have a gut sense this is not needed.
I havent tried it yet, but I am willing to bet that most programs for mac will just start if you click on them. Again, need some knowledge and I dont know whwere to get it.
I really want to run migration assistant so I can just port over all my odd settings; however, I have no idea what control I will have over the actual import.
I actually dont want to physically move any programs just yet. In fact, I want to use most of my non-Apple, personally-installel applications from the HDD. The only program that might be VERY useful to migrate to the SSD would be parallels and the windows VM I keep for VPN and PC-only programs as it is very slow. MAYBE MSoffice as those programs are slow to start up. Also, maybe aperature if it needs to be installed on the ssd to have it's swapfile on that drive. On second thought, that is fine where it is.
I am willing to just get in there and try it out, but I dont want to screw up my HDD install. I would like the separate OS instances to play nice with each other and I am not sure that will happen if i start calling applications from either one (though, obviously, not at the same time.)
So where could I discover what my bounderies are with this situation? Any "best practices?"
*I do want to keep the discussion off the topic of use of expresscard ssd for boot drives, but I felt I should comment further. They have thier pros and cons. I would not be surprised if my new drive fails (also not surprised if it lasts 10xexpected RW cycles.) Nevertheless, the speed is just absolutely amazing. Night and day difference on the "feel" of boot and program load. You can look up the benchmarks if you are inclined.

Thank you for the fast response.
Regarding use of the applications, is it your opinion that simply opening most applications by double-clicking should be sufficient to use them with their current settings. i.e., internal references to ~library/application support/relevant program.plist?
If so, is this universally true, i.e., any and all programs will work?
Regarding migrating settings, are you saying that I can import all my settings WITHOUT importing the programs?
Sorry for my being dense, and supplying a wall of text in the OP.

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