Unless you're really fast, it's better to ignore hitting the big notes for full value and alt it like as if the big note is a regular one. However, if the big note and the next note are different colours, treat the big note like you alted and the next note after should be whatever hand you used to hit the previous note before the big note.
If something like dKd (red, big blue, red) comes up, use whatever your dominant finger is on the first note and then both your other fingers to hit the big blue note, then hit the last d with whatever your dominant finger is, the same finger you used to hit the first d.