So while I am 100% sympathetic to your plight (because I went through exactly the same thing earlier this year) the best advice I can give you is:

1) avoid multi-vendor flying as much as possible.
2) never, ever, ever expect airline 'A' to accept any responsibility for anything that happened to you while flying airline 'B'. If you're on A1001 and your B2002 flight misses, they just don't care.
3) leave lots of extra time to connect on these type itineraries -- basically just assume that regardless of the airlines "partner" status they will do nothing except point fingers at each other.
4) if you're trying to do any kind of cross-airline award/upgrade, etc. be prepared to call lots of different agents, talk to different airlines one right after another and be told different things, and be ready for lots of searching/asking on FT to get help.

Things really shouldn't be this way, but all my experiences show that they are, and trying to get things changed just seems like banging my head into a very thick, very well established concrete wall. ;-(