First, check with CO again - they should be able to check your bags to the final destination. I was allways able to do that - even with different airlines and different tickets.

If you still cannot, immigration sometimes has long lines in HKG - but even then it should not take more than 40 min (this was my worst case) to get thru - usually it is just 5 to 10.
Also check: there are two immigration areas, one left and one right, around a 2 min walk between the areas. It does not matter which one you use - they both end up in the same baggage hall - and sometimes lines on one side are significantly shorter.
If it takes long to go thru immigration your luggage should be waiting for you. There is never a line at customs - walk thru / green channel as you see it in Europe. They rarely stop anybody - and usually they stop only people who look local.

HKG is well organized, very well posted and one of the easiest airports. So 2 hours should be plenty of time.