Hi Jonathan,
There are basically two ways to type accented characters:
• The traditional one is to type an accent key first, then the key for the base letter: this is the "dead key method"
• A newer way is to first type the base character, then a CDM. It’s a more flexible way, because you can easily stack accents, but it’s not universally supported yet.
Which one is better for you depends largely on taste, but also on the number of accents and accented characters you need to incorporate.
As you have chosen the dead-key method already, you may want to keep that for the last combination you need to make: U̇ and u̇.
To include these two letters, the only thing different from precomposed letters that have a Unicode number is that here, instead of the usual typed character or Unicode number, you specify 2 Unicode numbers as the output:
U ̇ = U+0055, U+0307
u ̇ = U+0075, U+0307
The above are hexadecimal numbers, which you can enter as follows in Ukelele (see the PDF manual, section 3.1.3 on page 7):
U̇
u̇