I went through a few years ago - nothing to it. Ii went through on Canadian side and you don't have to check in with customs since you're not going ashore. I don't think you want to be in there with the 1000 footers on the US side. Besides you might have to wait several hours on the US because they're unlikley to pump all that water for just your boat.
I assume you're staying on the southern shore. If so, it's 90 miles to the next port (Grand Marais) so be prepared for a fairly long passage.