My understanding is that if you don't enter or exit the Three Sisters Wllderness via the Obsidian Trail and stay on the PCT when in the special permit area, you don't need a special permit, just the one you fill out at the trailhead. Only the Willamette National Forest (on the west side of the Three Sisters) requires those permits, and only for that specific. If you enter/exit the wilderness from the Deschutes National Forest (east side, including the trailhead at McKenzie Pass), you're fine to do the loop--at least that's what the Deschutes NF rangers will tell you. I would presume they'd get plenty of feedback from ticketed hikers and Willamette NF rangers if that weren't true! Just stay on the PCT, not the Obsidian Trail, when going through that area.

The permits for the special use areas of the Willamette National Forest are now available only online (check their website for details). You can no longer get them at the ranger station. You also now have to pay a fee to the private concessionaire that now handles those permits, with no refund if you cancel. This particular ripoff just started this year. My understanding is that this change has been mandated by the USFS bureaucracy at the national level, so if you California folks haven't seen it yet, you will soon.

Up here in the PNW, the only places requiring special permits in national forests (as opposed to national parks, different federal agency, lots more bureaucracy) are a couple of high impact areas in Oregon's Willamette National Forest (Obsidian in Three Sisters Wilderness and Pamelia Lake in Mt. Jefferson) and Washington's Enchantment Lakes area in the Alpine Lakes Wilderness of Washington. Those all have limited permits in hopes of keeping those places from being loved to death. For all other USFS wilderness areas, you just fill out a free permit at the wilderness boundary or (sometimes) at the trailhead. Yes, rangers do want to see those, and you can get a ticket if you don't have one. The primary purpose of those free permits is to track usage, an important part of trying to justify the local USFS budget. That's therefore good reason for you to fill them out!

You do, of course, have to pay to park at most USFS trailheads up here in the PNW or have a Northwest Forest Pass or America the Beautiful Pass or Senior Pass (the last is a marvelous bargain for those of us age 62 and over). Due to vandalism of the fee boxes, at most trailheads you now need to purchase the permit ahead of time because there is often no way to pay at the trailhead. The USFS is ignoring last year's 9th Circuit Court decision, evidently hoping it will go away. In other words, you could probably fight a trailhead parking ticket successfully, if you can afford the hassle and the legal fees. Since I have the Senior (formerly Golden Age) pass and do generally use the trailhead facilities (the privy), I just go ahead and hang my Senior Pass as required.