Kelly,
I am sure there are several ways of accounting for the loss up to these pots (and would love to hear from the masses about what they might do), but one way is to definitely use the Spot elevations tool. As shown in the Power Tip link below, you can place these spots around your irrigation plan and make sure to check the "Use Spot Elevations" option when sizing your laterals and mainline.
While I am not 100% on the design layout and equipment you used, I am assuming that you should have enough room to place different spot elevations right next to the different equipment (head vs. valve) so the system recognizes the elevation difference from valve to furthest head.
If you find this to be challenging or have questions as you go, please reach back out in a tech support ticket and we can figure out another solution for you!
Power Tip- Spot Elevations In Irrigation