If my 1099b indicates for box 12 that it includes the amount from line 13, should I net the 2 amounts to report box 12 and report line 13 as well?

No, it does not appear you should do that.  The 1099-B is a composite form and has multiple sections, one of which is the 1099-DIV section.  Box 12, on Form 1099-DIV, contains all exempt interest dividends and it includes the box 13 amount which is specified private activity bond interest dividends.  Because the box 13 amount is already included in box 12, there is no need to net them.  

The box 13 amounts are subject to the alternative minimum tax.  If the AMT applies to you, you may need to refer to box 13.  

If you are referencing another section of your 1099-B, please provide that additional information. 

@Celery63