Hi Yehuda,
If it's about some command-line parameters passed from the master application, you can specify them via the "Run | Run Parameters" main menu item in AQtime. If this approach is not acceptable anyway, as an alternative, you can request a trial version of AQtime Pro (
http://smartbear.com/products/development-tools/performance-profiling/sign-up/) and use the Attach to Process feature, which is not available in AQtime Standard. If you're interested in this approach, let me know - I'll give you steps for that.