Putting money aside through a second account is great and becomes a bit of a 'prize' if your expected tax bill is lower than your actual tax bill.
That said, the above works better for low capital investment businesses like consulting and services and is harder when you sell products.
First and foremost, an accounting system is necessary. There are great free ones out there that will link with your bank accounts and credit cards. Invest a few hours and set this up.
If the year has elapsed and you have a large bill, the best way to legally reduce it is through a corporate 401(k). You can make contributions after the new year for the previous year and the caps are quite high. The downside of the above is you cannot reinvest this money in the business but, as I see it, it's either staying with you or going to Uncle Sam.