You have chosen a good time to go - high pressure will be moving in from Tuesday. What time are you arriving? I am working in the CI's later this week, and will be in St Peter Port until 3pm Thursday.
Lots of great places to visit around Guernsey and the Harbour/Marina is really well sheltered. I am no expert, but please read up a bit, as there a lots of underwater rocks etc - I suggest you buy and study a chart before heading out. I am sure somebody will be able to offer better advice than that though.
Try this link as a start for boating in Guernsey; it includes a downloadable map of the harbour etc.