Just went through the process and the FCC website I agree is about as clear as mud. The good news, I can give you the benefit of my vast (IE one and only) experience. Also, they have a phone
number for help where you immediately reach a real person that actually understands the process and will help.
First, you will want two licenses, one the ships license
and one is the operator's permit
As I recall
1. Go to the website and sign up for your FRN (FCC Registration
Number). That part was fairly simple. https://apps.fcc.gov/coresWeb/publicHome.do
2. Log in with your FRN, go to the online forms and fill in a form 605, I think you have to do it twice, once for each license but not certain about this.
3. When filling in the 605 you select license type SA - Ship Recreational or Voluntary for the ships station license and license type RR - for restricted operator's license. When filling in the SA form just ask for the license to cover everything they list. Doesn't cost extra and doesn't add any additional risks, liabilities or responsibilities.
4. Fill in form 159 to send payment.
5. In a day or so you will get an email
from the FCC with a link to your official license. Download, save somewhere for future reference and print a copy for the boat.