You can credit to one FF program. If and how they will credit, depends on who is marketing the flight (i.e. the booked flight number) and who is operating the flight.

In any case, there's generally no point in spreading your miles across multiple programs within the same alliance (unless you generate a lot of miles anyway, there is a double/tripple miles offer on one program, or if you plan to change anyway). If you only earn a couple of miles and spread them across 2, 3, or even more programs, you'll have small amounts sitting around and going to waste because you don't have enough in each program to redeem them.

Alternatively to using wheretocredit, you can check out how much miles you get by going to the website of your FFP.