My sister and I just did this a few weeks ago from the Polynesian marina. We had a great time! Yes, you can go all over Seven Seas Lagoon and cross the man made "bridge" over to Bay Lake.
When you are on the monorail, near the Contemporary, you can see this water bridge that has a road going underneath it. However, I was disappointed that when we crossed on this water bridge in the Sea Raycers, you can't tell you are going over anything and that there is a road underneath you. You have to really slow down in this "no wake" area.
The old Discovery Island is over on Bay Lake and you go right by the Contemporary. You can also see the Wilderness Lodge but aren't suppose to go in too close unless heading for their marina.
You have to be careful to watch out for all the other Sea Raycers, the smaller water launches that take resort guests from MK, GF, Poly and back. Also, the larger ferries that run between the TTC and the MK. There may also be larger pleasure boats that guests have rented. And of course, the marina patrol boats that go FAST! It's alot to look out for so you have to be careful.
For those reasons we found Seven Seas Lagoon to be busier with water traffic than Bay Lake. But not unworkable.
You also have to go slowly around the other boats and keep your distance. And there are areas near each resort and the MK that you aren't allowed into unless you are docking at a resort marina.
I'm sure some wild drivers would like to skip across the wake left by other boats but you really aren't suppose to take big chances this way. If you drive in a manner they've instructed you not to, they will make you get off the lakes and take away any future watercraft privileges. You can tip these boats. They said it happens all the time but usually because someone was intentionally driving crazy.
We found it a bit frightening to hit some of the larger wakes head on, you could most definitely tip your boat if you don't 1) slow down and 2) turn into the direction of the wake rather than trying to cross the waves head on.
I found you can really go full speed better over in areas of Bay Lake. That was FUN!
We stayed out 45 minutes and felt that was a good amount of time. I might have stayed out for an hour but my sister wanted to come in. After awhile, there is nowhere else to go - I kind of wish you could go into even more lakes and further afield.
People on these boards have said it is faster with only one person and that may be so. However, we found it to be fine with two. They instruct that if you are in two boats, you aren't suppose to stop or slow down close to each other to talk. Although I did see a man and his son in two boats doing this.
We liked being in the same boat to talk to each other.
I would highly recommend this activity. It was a blast!