Ciao all!
This is my first post and I am pretty excited because I planning the JMT for this September.
For various reason I decided to chicken out Whitney and enter from Onion Valley. I will be flying to SF with a friend and we want to avoid renting a car I already went this way few times to Yosemite and I know I can arrive almost easy to Mammoth but how to arrive to Onion?
Also I am really not clear on where I need to get the permit(s)? please help!

You get your permits from here: http://www.recreation.gov/

They are issued for Inyo National Forest. Onion Valley can be 'hit-or-miss' for getting a ride. Lots of day hikers seem to come back down and exit in the afternoon. Have a great trip. It should be pretty dry and mozzie-free in Sept.

This mean I will hike to Yosemite with the permit for Inyo alone?

Yes. On recreation.gov,

click on Inyo National Forest wilderness permits;
entry trail is Kearsarge Pass;
exit is Happy Isles/Yosemite.

You will be able to pick up your permit at any Inyo National Forest office - Lee Vining, Mammoth, Bishop, or Lone Pine. I think recreation.gov asks you which of those offices you will be picking up your permit at. Don't pick Lone Pine. If you are sure you are going to be in the town of Mammoth Lakes, maybe plan to pick it up there. Or if you want more updated conditions on the southern sections of the JMT, plan to pick it up in Bishop (although that might interrupt a good hitchhike).

From Mammoth I would just hitchhike to Independence and then to Onion Valley from there.

It'll be fantastic in September, not as crowded. A little dry this year, though.

- Elizabeth