So... the wife and I are planning a trip for just us this fall. I have a LIS South permit for September 13th. LIS South is one permit every other day. The permits for September 9 & 11 are taken. I'm worried about heading to Bootleg Lake and there not being a campsite. there's only two on the lake. It's another 3-3 1/2 hours to the next campsite with a half mile and a mile portage along the route.

So question is where do most people head to out of LIS South? What do you think my odds are that there will be a campsite available with both permits gone the days before our entry?

I just need to get her on a lake to catch fish. I don't care if I catch or not, it's about her enjoying the trip. I've heard that Bootleg can be a pretty good lake for that. Any other thoughts or ideas?

I don't think you will have too much to worry about in mid September. I stayed on Bootleg several night a few years ago and didn't see a soul. Most people will either head toward Little Trout, paddle back to the entry point, or continue to Cummings; My guess is that you won't see anyone. There used to be an "unofficial Site" on the south end of Bootleg if you were to get into trouble (not that I'm recommending using it). Water levels on the Little Pony might be low in September and you might want to take the other portage in.

They've also added a campsite right before the river splits after the 85rd portage if you don't have updated maps. I think they did that last year or the year before. I've only done part of LIS south, I usually head north. I've looked into going south, and it was even on the list for our trip this year, but there is still too much of EP 14 we haven't explored yet.
In 2018 we did a day trip down to the first portage. My uncle pulled a monster pike out of the hole right below the waterfall. Something peaceful about the river. Have fun and post a trip report!

We went that way some time ago and I remember being worried that permits were taken for the whole week prior. We had Bootleg all to ourselves (though we only spent one night there before pushing through to Little Trout). That was a quick 4 day trip and 3 of the 4 days we saw no other people.

A few years back we took a day trip to the falls at the first portage and saw a couple of guys heading in early afternoon. We also met a father and son heading out. Then on our way out we met a group of college age kids just getting their gear together at the parking lot around 4:30. So many more people than the last time we were there and at least one group cheating the system!