In dual mode (what most ppl use), if you're watching a show on TV2 and a timer is in place, yes - it will interrupt the show you're watching to record the timer.
In single mode (what I use most of the time), you can be watching a show on TV2 and the timer will record in the background, not interrupting your show. But in order for that to work, TV1 has to watch the same show TV2 is watching, and vice versa.