Get permit now when planning for remodel?

Remodeling newbie here hoping for advice from more seasoned homeowners. I browsed the BPN site on home remodels but didn't see anything specifically on this question. 

We have in mind several remodel projects for our house in Berkeley. The highest priority is to tear out an existing addition to our house and have a new addition built on the same footprint, but half a level higher than the current addition, to be level with the main floor of the house (the current addition is ground level, which is half a level below the living room/dining room/kitchen). For various reasons, we probably wouldn't want to do this work for at least 2 years, possibly 3-5 years. But I've heard the permitting process can take so long, that I wonder if we should start working now with an architect to draw up some plans. Is it possible to have a project permitted but hold off on the construction for some period of time? Or does it all need to happen in quick succession? How much can we expect to spend working with an architect just to have some plans created?

On a related note, does the architect handle the permit application process, or is all or some of that left to the contractor? 

Anything else this total newbie should keep in mind as I begin this process? Many thanks!

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To begin with, you may want to check with the city or an architect if your project even needs a permit. It's not adding new space. For example, a kitchen or bath remodel can often be done without permits. If you haven't yet, I would strongly recommend just talking to the city permit desk officer about these topics first. 

I can only speak from my experience in Albany, not Berkeley. Permitting takes 6-9 months (not 2-3 years). An approved permit must be issued ('pulled') within a year or it lapses. The permit application is typically submitted by an architect (who represents you at city hearings etc) but issued to a contractor. You can issue a permit to yourself as homeowner but there are certain risks associated with this: Also, Albany requires a construction bond (around $2000) which is only refunded after construction is complete and the project passes final inspection - this is to motivate people to finish their projects.

In your situation, you could possibly get a permit application approved, issued, and then schedule construction 1-2 years later; assuming that a contractor would agree to those terms and you're willing to wait to get your bond back (and your project done). 

How much you spend on an architect can vary widely depending on the project scope, but if there's structural work involved, expect $10-20k on design/survey/engineering fees and another $10-20k in city permit fees, all before a spade even hits the ground.