I had to book a trip HYD-JFK-HYD. When I was booking it as a roundtrip however, I was unable to get the specific flight pair I wanted for the outbound (529 connecting to 203). The inbound was fine and giving me the flights I wanted, so I ended up searching it as a multicity:
HYD-DXB/DXB-JFK/JFK-HYD. Priced out the same as it would've been as a roundtrip and I was able to choose the specific flights I wanted so I booked it as a multicity. Connection in DXB is still 2.5 hours. I just want to make sure that booking as a multicity won't make checking bags through or getting BP/s for both segments an issue?
Any help is appreciated.

Thanks