On my 1099-R from Vanguard there are 2 entries in Box 1. Do I combine them and enter the total in Box 1 and Box 2?

Some financial institutions report each security/account separately - others just report the totals..   You can enter as two 1099-R's or just the combined total in a single 1099-R.

If both box 1 entries are reported on the same Form 1099-R, then those can be combined.  

Report box 2 exactly as it was reported to you.  If there are two numbers there as well, you can combine them.  If box 2 is blank, leave it that way.

If you have a question about what is being reported on the 1099-R, contact Vanguard for further information.