Question 1: The modified letters WILL need to be on the Special Symbols page as well as in the pronunciation key. Just the symbols are listed - the letters the symbols modify should not be on the Special Symbols list. And yes, the dot locator should precede those symbols.
Part 1 - use a numeric or letter key as before.
Part 2 - when you define the letter or number in the key listing, state what it applies to. You can no longer use the terminator indicator as a terminator...it would conflict with other UEB symbols.