Stockholm Archipelago

I'd first decide what island you want to visit.

Waxholmsbolaget operates ferries to many of the islands. You buy your ticket on board. You can check schedules and prices on their website.
http://www.waxholmsbolaget.se/visitor/archipelago-traffic/tickets-prices/

Cinderella boats also has trips to some islands.
http://www.stromma.se/en/stockholm/cinderella-boats/

The Archipelago Foundation has info on the islands with some helpful tips on getting to each island and some accommodarion info:
http://archipelagofoundation.se
Scroll down to the bottom and select the island you want to visit.

I've only visited Grinda and Utö, both as day trips. If you are staying overnight, you might want to visit one of the islands that is further out. Sandhamn and Finnhamn are both popular.

Thanks I'll check out those sites!

I didn't overnight in the Archipelago, but I did take the canal boat day trip out to Sandhamn. Very beautiful and peaceful excursion.

We are in the archipelago now; actually sitting on a Cinderella ferry! We've spent 3 days in the archipelago and had a great time.

First, no reservations were necessary that we found, and we are traveling at a very busy time. We even decided to have dinner on our way back to Stockholm this evening and did not need reservations for the restaurant on board (although most people did have them).

Second, Vaxholm is a popular site and easy to get to from Stockholm. It's a nice place to spend a day - there's a castle/fort to visit and you can stay overnight in the B&B there (we did). It was more like a hostel so lower expectations from what you might expect a normal B&B to be like.

At Vaxholm is a ferry information center and the staff there were very helpful in helping us understand the ferries as we also went to Svartso, Grinda, and Sandhamn. The ferry schedules were confusing to us, but I believe you can print out the information and spend some time with it before you go.

Have fun!