No, the currents don't mimic each other. This is useful to remember because often the canal is flowing backwards of the main current. You can see this visualized nicely on NOAA Charts with animated currents. Silverlight Design and Development
(there is also a Windows Phone version of this called Nautical Charts if you have a Windows Phone).
I haven't anchored in either, but they are both quite exposed. I did anchor in an even more exposed location north of Kingston and south of Point No Point, but I barely slept and wouldn't recommend it. We used two anchors, one oversized claw off of the bow and a correctly sized Danforth on the stern.
You might find Alex Wetmore is always busy with something… » Blog Archive » Sailing to the San Juans
interesting if you are planning a trip north out of Seattle. It has notes from my trip to the San Juans last summer. A map showing where we slept can be found here:
Map created by GPS Visualizer
If you time your passage correctly (as we did on day 2) you can make serious miles by using the currents.