Both of these utilities are run outside of P3D and can then be left alone – as the modifications stay in place for each P3D session (P3D needs to be closed when applying presets).
IMPORTANT: I’ve now upgraded to P3Dv5 HF2 but, sadly, did not have room on my system to retain my old P3Dv4.5. This means I can no longer develop or test new PTA or Tomatoshade presets, as neither have been updated for P3Dv5. Anyone that has updated to P3Dv4.5 Hotfix3 should try using the latest/last presets available here and use them as a starting point. P3D lighting/shading doesn’t change that much between versions, so you should be roughly in the same ball park.
XP11 also allows shader mods when used with either/both the commercial xVision (PTA clone) or freeware FlywithLUA.