The Swiss Rail pass is not accepted for travel on Lago Maggiore as most of the lake is in Italy. Instead you buy tickets from Navigazione Lago Maggiore, the company that traverses the lake from Locarno in the north to Stresa and Arona in the south. 

For an idea of prices...A one way ticket from Ascona to Locarno is 6 CHF (just under $6 Can). If you plan to travel a lot on the lake, you can buy boat passes for a day or a week.  

The Lago Maggiore Express gives an overview of the lake and includes a fabulous train trip. Round trip cost is 42 CHF. Every day but Wednesday you take the boat to Stresa and return via train (vice versa on Wednesdays). It's independent travel as you can catch the boat and train at several times. Best to start out early, though, in order to have time for Stresa or other lake towns.

To catch the train in Locarno, you go to the undergound station just back of the regular station.  The Centovalli Railway goes through centivalli (valley of a hundred valleys) from Locarno in Switzerland to Domodossala in Italy. This is one of the most spectacular train rides anywhere -- mile after mile of eye-popping gorges with rushing rivers and towns hanging onto hillsides.  In Domodossola (a maze of platforms with people rushing everywhere to catch trains to Berne, Geneva, etc.) you change trains for Stresa. 

Once in Stresa head downhill to find the centre of town and the boats to the Borromean Islands. There are no signs but once at the lakeside follow the lake to the right to get to the main boat docks.  There is a docking area to the left but it is a long walk along the lake and hard to find. Stresa is a picturesque town with green hills in the background and the Borromean Islands lying a short distance offshore.

The Lago Maggiore Express includes a boat trip to Isole Bella and one back to Locarno, with stops along the way at several lake towns. Isole Bella is touted as one of the most beautiful Borromean Islands, which it is. The 17th C castle and gardens are sensational. But the rest of the grounds are over-commercialized. The island is loaded with wall-to-wall souvenir shops and pricey restaurants. All this in the midst of great beauty....