Hi Adrian,
I think that the easiest way is like this:
-- You will need to create two AQtime projects (
http://support.smartbear.com/viewarticle/43517/), one per each application and set up these projects so they use proper binaries with corresponding debug information and sources;
-- Then you will need to execute profiling run for both applications using the same profilers and profiling areas setup (
http://support.smartbear.com/viewarticle/43100/); (there are recordings at
http://support.smartbear.com/screencasts/aqtime/ that might appear to be useful)
-- Finally, you should export profiling results to some database (
http://support.smartbear.com/viewarticle/43461/) and compare results using database reporting means.
Alternative approach if profiling results are not huge (i.e. if you identified several problematic areas within your applications and profile them one by one) is to compare results manually by opening them side by side in AQtime running on separate machines (if I remember correctly, two Aqtime instances cannot be started on the same machine).
Also you may consider to have one AQtime project and remap included profiled binaries from first application to second one and back. In this case you will be able to compare profiling results using AQtime's means (
http://support.smartbear.com/viewarticle/43305/), but I am not sure if this way is more convenient when compared with two AQtime projects and results export to the database.
