Why on the 1040 it lists the total income on the 1099R. For example, it doesn’t show my pension or my IRA 1099R listed separately. Just gives one total on the 1040 form?

Line 4a shows IRA distribution and 5a the pension. Be sure that you checked the box on your 1099-R indicating an IRA withdrawal if you had one. 

Yes, all your 1099-R income shows on Form 1040, Line 5a.  The Taxable Amount shows on Line 5b.

 

When you entered your 1099-R  for your IRA Distribution, make sure the IRA/SEP/Simple box is checked (after Box 7) and it should show on Line 4a/b instead.

 

For tax purposes, they are taxed the same, though.

 

Here's more info on Form 1099-R.