In Yosemite, you get one wilderness permit from a permit office, and you enter the wilderness at a designated place mentioned on that permit. Note that many trails have trailhead quotas. The most popular trails may have the quota filled up before you get there. So, for a high priority trip, you may seek to pay a few bucks for a wilderness permit reservation. You can telephone the permit office and do all of this in advance, but it helps an awful lot of you know exactly where you are going. Once you exit from that, the permit is finished. You would need to get another permit for another destination.
So, if you have five destinations in mind, you may seek to tie all of those together into one trip (hence, one permit). Your five destinations are kind of scattered out, so one trip may be impractical. You could go from Yosemite Valley to Glacier Point to Cathedral Lakes to Tuolumne Meadows in one trip of two days. The Mariposa Grove is out of the way from there, and it is the sort of place where you can drive in, see what you want in a couple of hours, and then you are done.
First, study the park map and note where the places are and where the trails are. Second, contact the permit station for a reservation.
Also, keep in mind that virtually everyplace will require bear canisters for food storage. Often times, the permit station can rent you one or more when you actually pick up your permit. More bucks.
EDIT: Let me add that Yosemite Valley is not wilderness. It is a starting point, or maybe just a place to take photos while you are amongst thousands of your closest fellow tourists. Well, for that matter, Glacier Point isn't either. It is a great place to go to do some photography from just prior to sunrise until about 9 a.m., and then the tour buses will arrive, spewing diesel exhaust.