The 4 places you mention are the only places in Thailand that TE will do the 90 day report on your behalf.
It means 2 trips. Once to drop the passports off and you return a few days later to collect them again.
A TE yearly extension can be done in any immigration office.
If you want TE to hold your hand and go with you for an extension, it isn't free. They will meet you at Bangkok, Phuket,Pattaya or Chiang Mai immigration.
It's 2000 baht per person for the TE service plus 1900 baht per person for the extension.
Another thing. If you want TE to provide any of those services, you need to make sure you lodge a completely new TM30 every 12 months and have the printout in your passport from immigration or TE simply won't entertain you.