If you by material at a Big Box and get taxed then the tax is paid. You can only recoup the tax from your customer that you paid.
No, you can claim a credit on your Sales Tax return. But most of us just add the tax to the cost of the material because it's too difficult to keep track. Yeah, the customer gets charged tax on the total of the material, plus the tax you paid for it when you bought it, plus your markup, but that's life.
I have never collected sales tax in NYS. According to the wording of my invoices, everything I do is a capital improvement.
A friend of mine who is also an EC has been in business for over forty years. When he started the business, the accountant he had at the time told him that he didn't need to collect sales tax which he never did. If I were in his shoes, I wouldn't be able to sleep at night worrying about getting a letter from the NYS Department to Taxation and Finance because they want to do an audit. Most of us do at least a fair amount of service work that we need to collect tax on. I can tell you that NYS is worse than the feds. If you can't justify your numbers they will just assess you whatever they think a business like yours should have collected plus penalties and interest. Then it's up to you and your CPA to prove them wrong. And they can go back seven years or even more.
A number of years ago I got a letter from the Connecticut DRS. I'm across the boarder in NY and I had a customer who had a location in CT which I rarely had to go to. What happened was apparently that company was audited and the auditors came across an invoice from me that didn't include sales tax. (See how they get you?) So now they are on to me and I not only had to register to collect CT tax and file every January, I had to go back six years. Unlike draconian NY, they only wanted me to pay the taxes I didn't collect and didn't assess interest or penalties. Fortunately that amounted to the tax on only a few minor service calls.
According to the wording of my invoices, everything I do is a capital improvement. Yeah, well I don't think that's good enough. Can you truthfully say that all you do or have ever done is new construction? All they have to do is look at your invoices to see what you have done and if anything looks like repair or service work (or is unclear) they're going to say you should have collected the tax on it. And if something really is a Capital Improvement you better be able to provide a properly filled out and signed Certificate of Capital Improvement for EVERY job.
Really, why would you not want to collect sales tax? If you have a certificate of authority and a tax ID you are required by law to do so. Any bookkeeping system like Quickbooks does a good job of tracking your sales tax. You remit quarterly so if you have a sizable amount of tax collected, you can even use that money until it's due. And they even pay you a percentage for being a tax collector.
Let me tell you, NYS is hurting for money. I wouldn't mess with them. But unfortunately like my friend, if you start collecting now after all those years you could be opening a can of worms.
-Hal