Hi Mike,
Answers
1) If you an SDK config you are guaranteed that it will point to the correct U-boot and kernel. That config is the same exact config used to build the specific SDK.
The longer answer is that we use a combination of PREFERRED_VERSIONS and PREFERRED_PROVIDERS. meta-arago-distro/conf/distro/include/arago-prefs.inc and machine include files meta-ti//conf/machine/include/ti33x.inc are the typical places that we use to insure that the correct recipe version and recipe is used.
2) Yes.
3) Yes. As long as you increase the PR for the recipe that you tweaked the next time you build it directly or indirectly (ex filesystem image) the recipe will be rebuilt.
4) Yes
I would highly recommend that you run through the OE training atleast once and stick with SDK 6.0 for the training. There are parts of the training and labs that will differ when ran on SDK 7.0 and unless you understand some of the basics you will end up getting stuck. However, once you gone through the training it will be trivial for you to apply what you learn on SDK 7.