You have a misconception/misunderstanding about threads and applications. You don't specify an application to "run in a different thread". You specify a specific task to run as a separate thread. An application can (and usually does) create multiple threads, and most of this automatic. You can explicitly create a new thread for a specific task that may take a while and you want to run it in the background. With an application you can specify processor affinity, which is something else alltogether. This essentially allows an application (if capable) to make use of multiple processors, or it specifically limits the application to a single processor (if, for example, the application was written at a time when there were no multi-core CPUs).
That said, your question cannot be answered without a whole of further details. What is your application doing? Is it doing a lot of calculations? Is it collecting a lot of data? Is is drawing a lot of things? Is it playing music? Do you have other processes running that are chopping up memory? Is it... I think you get the picture.
