It's a tough judgement call. If you wait you won't get penalties and interest if you are right and they eventually agree. But if you're wrong or they don't agree you will at least be paying interest and maybe a penalty.
It is safer to pay and then deal. It is very very very hard to get hold of the IRS these days. Written correspondence also takes forever.
In any case, I would expect that if could take months to resolve and could easily be a year+. I know that's pessimistic, but that's been my experience recently with anything that is not automated.
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