A few people have said it already, but I'd like to reiterate:
Don't expect software to be able to do this for you. Tax laws change every year, both federal and state. Requirements for corporate filings change every year. Payroll requirements change every year (withholding amounts for FICA, FUTA, unemployment, health insurance requirements, etc).
I have an S-corp, but I don't do any of this myself.
I have a payroll service that costs $50 or so per month. For that cost, they do direct deposit, tax withholding, and also file quarterly 941 forms and prepare W-2s at the end of the year. All deductions are calculated by them, and their guarantee is that if they make a mistake, they take liability for it - ie, they'll pay any penalties or interest that arise as a result.
I have a lawyer who charges less than $200/year to prepare corporate filings. Additionally, they provide me with a list of changes to corporate laws over the course of the year. They highlight anything that may be important for me as a small business owner.
I have a CPA who prepares the corporate tax return. I do the day-to-day accounting (I happen to have Peachtree for Windows, I couldn't find anything open source or Linux based in 2000 when I started this business), but the CPA checks things over and prepares the corporate return and shareholder K-1 forms. This costs about $1000/year.
Overall, I pay roughly $2000/year for all of these services. I think this is well worth it, since I not only don't have to spend the time actually doing this work, but I also don't have to spend the time learning how I need to do it differently every year. I also get some measure of effective insurance, at least with the payroll company, since they are responsible for any mistakes they might make (they haven't made any yet).
I note that most of the question was really directed at legal questions. You can certainly get boilerplate contracts from several places. You may want to find a local lawyer and have them write you one. Get a confidentiality agreement, a subcontractor agreement, and a contract for services (that you provide). Once you have those, you can essentially reuse them for future contracts. There aren't a lot of requirements for meeting minutes (though one thing you should watch out for is that you are required to send a notice of shareholder meetings some 30 days before they're scheduled, or you need to have a "waiver of notice" form signed by all the shareholders. Of course this may not be true in your state) - just a list of people present, a very simple list of topics covered (summaries of the conversation are good, but are not necessary), and the dated signatures of the corporate secretary and president, who in my state can't be the same person.
The bottom line is that there is a lot of expertise needed to do these things right and keep up with all the annual changes. The cost of hiring experts is not that high, so it should be pretty close to a no-brainer.