As a general rule, use the same individuals as references for each nominating source. This will make your life easier in keeping track of who has done what.
Per GoforSpaatz, each nomination source may have a different requirement regarding references (for example, on congressman might want 2 and the Senator may require 3), make sure you know their process.
As for us, DD had all the LORs returned to her and then she sent the entire completed package to the MOC. Though the LORs were in their own individual envelopes, the packet as a whole was submitted to each MOC. (Make a copy of everything before submitting the package)