Originally Posted by
cbr600f4i2
But whether it's an AA flight number or Alaska flight number, I can NEVER check in online, or reserve seats for these flights

I can't check in online with AA or with Alaska's sites.
It's not specifically whether the booking took place on aa.com, or on a third-party site. However, if booking an AA-coded segment on aa.com, you "should" receive a seat assignment, provided that non-premium seats are available.