Hi, Joyce.
I write about this for educational purposes only. It's not legal advice. If you need legal advice, I recommend Lic. Yuannie Arrollo Casillas in Ocean Park: 787-258-5566; licyac [at ] gmail.com. I've used her before and she's good.
To register an LLC or LLP (which are the company types I imagine you would want to use), you should register and pay online. This service wasn't available when I did my last incorporation so I'm not sure if it's reliable or not. Either way, you pay and you get a receipt so it would just be a matter of following up. Here is a link to the PR SOS Corporations Division: https://prcorpfiling.f1hst.com/Creation … lity.aspx.
If you're having problems using the online system, here is a link to the company organization forms that you can use to submit your paperwork the old-fashioned way: http://www2.pr.gov/agencias/estado/Page … Corp.aspx. If you go this route, I would not mail-in your paperwork. Take it personally to the PR SOS. The Secretary of State's Corporations Division is in Old San Juan. Go early in the morning. When I lived there, you'd notice a short line forming before the office even opens. This was/is because the "public servants" would stop accepting applications for forming a business after an hour or so, or a set limit of applications (like 15 or something ridiculously low). I don't know if Fortuno's administration was able to stop that practice or not. If not, I hope the new administration deals with it.
You'll quickly notice one of the many ways the PR government treats business owners and entrepreneurs like a vampire treats its victims: When you submit your paperwork, you have to choose one of I believe are three payment options for them to process your Certificate of Incorporation. The cheapest is $160 or thereabouts for what is supposed to take a few weeks, the next cheapest, if I recall correctly, is approximately $400 for a quicker turn-around, and then I believe there is even a more expensive option for two day incorporation. It's a shake-down. If you only pay the $100, they could sit on your application for as long as seven months, so make sure you go down there again. Don't just call - it would be a miracle if anyone actually answered the phone but as you may know, in PR it's all about face-to-face interaction if you want anything to get done.
You need your Certificate of Organization if you want to set up a business bank account (this is thanks to the Patriot Act). You'll also need to have your municipal business license in order to set up the bank account. I think Banco Santander PR has a list of exactly what you'll need on their website.
In addition, don't forget to register on the Compulsory Business Registry by July 15 of each year. This is handled by the Puerto Rico Trade and Export Company.
I'm very pessimistic about business ventures in PR. The government disdains business owners and punishes them as much as possible. They're viewed as cash-cows, not as risky enterprises that should be encouraged. Puerto Rico is where many good small businesses go to die. Then again, I'm a commercial bankruptcy attorney so perhaps I've simply seen too many failures. Good luck.