How are control characters handled in keyboard layouts?

Warmup question: What exactly is the difference between an "input method" and a "keyboard layout"?
Real question: What exactly happens when I switch keyboard layouts and enter control characters, and how can I change it?
I'll use as an example Hebrew-QWERTY and the "a" key. That key maps to Hebrew character aleph or א. What happens when I press control-a?
The Emacs text editor claims to receive a control-aleph, saying "^א is undefined". This is a very strange character: א with bit 26 set. It doesn't even have a Unicode codepoint.
TextEdit normally responds to control-a by moving to the start of the line. It doesn't do so with Hebrew-QWERTY in force, hence it's not getting a control-a. I have no idea what it is getting.
The goal, by the way, is to create a keyboard layout that does NOT change the mapping of control characters. I don't want control-a to send a useless control-aleph; I want it to send control-a as usual. But if I examine the Hebrew-QWERTY layout in (say) Ukelele, it knows nothing of control-aleph and claims to map control-a to itself as usual. Therefore something else is producing these weird control characters. Who?
If I'm hopelessly confused, please don't hesitate to say so. I wouldn't be surprised to learn that I'm missing something simple but crucial.

Tom Gewecke wrote:
Regarding control characters, you might try posting a query on the Ukelele page -- the fellow who makes that app knows a lot about how all this works.
Layout vs Method: Thanks for the clarification.
Ukelele: I've already posted to the Ukelele-users Google group, thus:
http://groups.google.com/group/ukelele-users/browse_thread/thread/b9c8aadfd6969c 15?hl=en
If that's what you mean by "the Ukelele page", I'm all set (assuming he replies). If you meant somewhere else, please let me know. I didn't find an Apple discussion forum specifically for Ukelele.

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