I have a non O and will soon do my 12 month extension of stay based on retirement. Will the extension of stay start the same day that I go to the Immigration and apply? Or will it start the day after my 90 day stamp in my passport expire ?

It will start when your current permission to stay ends.

It will start at the end of your current permitted to stay stamp.

Ok, thanks a lot. I will go 45 days days before (Bangkok) so it's good to know

Can I apply for a multiple re-entry permit at the same time? Or should I wait until I got approved and have the extension of stay stamp in my passport?

AFAIK you will need  to queue up at another window for the re-entry permit once your passport has been stamped with the extension of stay. But probably still worth doing in the same visit if you have the time.

Thank you

One more question. If I go 45 days before and do my extension of stay. Can I leave Thailand under those 45 days? Before the 12 month extension of stay have started ?

Only if you obtain a new re-entry permit first.  You get a new permitted to stay stamp immediately and re-entry permit must match that stamp.

Thanks a lot for all info