Some out-and-back overnights include Little Yosemite Valley that you mention.
And Yosemite Creek--you can backpack in from Tioga Road and head to the top of Upper Yosemite Falls and return. Or continue down the Yosemite Falls Trail and end up at Camp 4/Yosemite Lodge area in the Valley.
You have to be 4 miles from the trailhead before you can camp. Here's the rules:
http://www.nps.gov/yose/planyourvisit/wildregs.htmIf you have a wilderness permit you may camp in the Backpackers Campground (just north of North Pines Campground and just north of Tenaya Creek, across a footbridge). Not on most maps.
As far as Wilderness Permits are concerned, they don't care if you spent the night in Camp 4 or anywhere in Yosemite. You can get a permit the day you arrive if they have any available. More likely the trailheads you want are not available and you need to get a permit for the next day.