I suggest you check with your accountant as I think that separating these expenses is not correct or required.  The only way I know to separate them would be to have two different vendors and enter each part as a separate invoice.  

You can break out the portion of the invoice that is exempt from Form 1099 reporting on one or more separate distributions for the invoice.  When entering the exempt portion, click the "Exempt" button at the bottom of the invoice entry screen and that line item will be flagged and not reported for the 1099 amount.  The phrase "1099 Exempt" will appear below the distribution entry grid when the cursor is on a line that has been marked exempt. 

Art Minds
Senior Independent Consultant
Pasadena, California