Originally Posted by
ursine1
It sounds like you don't technically have a connecting flight, but rather two separate flights getting you to your final destination. In that case, yes, you will need to check in separately for each flight using the respective PRN at t-24, respectively for each. The flight number won't mean anything at check in; you just need the PNR(s).
Question: Why didn't you book the actual connecting flight, rather than two separate legs?
I know this is not the case for OP but i did this before when i needed 2 more segments to get a-list on like 12/29/12. I ended up booking SEA > SJC then SJC>SNA. worked out well in the end, I just needed to print two boarding passes with two different confirmation numbers.