I just submitted the FAFSA today!
He fills out the forms online, then a part asks for your information (gross income, etc.). You both end up signing with your ID's, but it's on the same online form. It'll guide you and tell you which places you need to sign and which places he needs to sign.
There's also a place where you can transfer the information over from the IRS where you filled out your taxes onto the forum to make things easier. Again, it'll prompt you when you get to this part and ask you for your FAFSA ID for both of you.