I am doing my son's taxes for the first time he is only 17, I get a check for him every month from SSD, he gets a separate SSA-1099 sent, do I add it to his taxes?

If he has other income to enter on his tax return, then the benefits reported on the SSA-1099 are entered on his tax return.  Make sure that you have indicated on his tax return that he can be claimed as a dependent.

I have entered his W-2 already but this is a SSA-1099 statement we get that says how much his payments came out to for the whole year. So when I get to t he point in his taxes of did he receive SSI benefits do I enter yes?

Yes, since he received a Form SSA-1099