Your best bet is to do some research on IRS.GOV for basic info. I personally think you need very good tax and legal counsel to help make sure you don't make mistakes.
We have an LLC. I run payroll and pay payroll taxes monthly through EFTPS, quarterly I file a 941 report and the TWC paperwork and any money due.
It is a lot to keep up with since I am not an accountant but I do all the accounting for our company. I have a Quickbooks tutor who owns her own bookkeeping business and she walks me through details and then my tax counsel checks everything.
I find it easy to work through Quickbooks. You get prompts on when it is time for something which helps me.
Again, I don't know how big your company is but my opinion is don't mess with the IRS and I pay my tax and legal counsel to help make sure everything we have is on the up and up. It is worth that extra money to me.
We only have hubby, myself and daughter with our company but it is getting fairly large and we're probably looking at moving the business out of the house and into an office. We have warehousing and a trucking company set up in Dallas and Houston with our products. I am constantly making sure all the t's are crossed just right and i's are dotted just right, especially when I am producing invoices, etc.
Good luck