I suffered with this once. We were going to New York via Gatwick and even though the journey was on one ticket the shuttle from Manchester to Gatwick was with BA and the onward flight to NYC with Continental. The outward flight was delayed so we got to check-in with Continental 5 minutes after the desk closed and they wouldn't let us on even though there was still 55 minutes before departure, they had our bags and knew we were at Gatwick!!! They were actually in the process of removing our bags from the plane whilst we were stood arguing at check-in! Dealing with a US airline probably didn't help us here I admit, but my experience suggests that they probably won't hold the flight. However, I think they'd be more likely to hold the connection if both parts of your journey were with the same airline.
Even though our bags were checked all the way through, we had to check in twice. Maybe you could ask to check in for the connecting flight at the same time as your first flight? Again, with it being 2 airlines, I don't know if this is possible. Also, you'd have more protection from a missed connection if your flights are all on the same ticket as it officially counts as the same journey. In our case, BA had to compensate us. If you have 2 tickets (eg. Manchester to Gatwick as one fare then Gatwick to NYC as an entirely different fare) then you've got no chance as the time between connections is your responsibility entirely.
The best bit of advice I can give you though is that if worst comes to worst and you do miss your connection but manage to arrange another flight to get you to your final destination, make sure that you re-confirm all of your return trip with the airlines. As we found to our cost, if you don't make a flight and then don't re-confirm the return, the airline will assume that you never reached your destination at all and cancel your ticket!