My question is; if I want to add the >> symbol do I just paste it in both the Soft Keys line and the Functions line at the same place?
That's right. Don't be afraid, this calc wants to be customized. If you break something (by, say, adding a name but not a corresponding function) and you wouldn't be able to figure out what went wrong, you can always revert it what it was before your modification, by going to Definition | Restore | Restore Calculator.
Changing the degree symbol is a great idea, except it suffers from the same problem as putting ->NUM on the keypad: it'll only be accessible when you have a single-line edit line. As soon as you switch to the multi-line editor, the iOS keyboard will cover it up. Of course, why not do both? Add it to a menu and replace an unused keypad key.
As for menus: you can create one from scratch, and delete unused ones. You could have a Favorites menu which contains all your most used functions and special keys, for example.