Good Run Guide automatically keeps track of your PB's for you. PB's are identified by comparing all the times you've logged for the same route name. You need to run a route at least twice for it to appear in your PB list and you need to ensure that the "Check for PB" box is ticked when logging your run if you want it to qualify as a potential PB.

If you've logged a PB but is doesn't appear in your PB list, you can check that the route name and "Check for PB" settings are correctly recorded by clicking on the Search Log Book button on the left to locate runs for a given route.

If a run shouldn't be on your PB list you can remove it be selecting Forget this PB or by selecting Forget all PB's for this route to remove all runs with the same route name from the PB list. This will not delete the runs from your Log Book, it will simply uncheck the "Check for PB" setting on these runs.