I may be wrong on this, but my impression is that the current workflow is that pickers cannot use junk information. Based on the how-to page ( Job: Micrograph Junk Detector (BETA) | CryoSPARC Guide ), I think that you have to run junk detector and if you want to filter particle picks, you can re-run junk detector after picking particles and it will remove any close to the junk masks, but it doesn’t use junk information during the particle picking process.
If you’re using hexaufoils and have lots of gold in your images, you may also want to check this thread out – your processing may be limited based on the amount of gold in the image, depending on the size of your camera (4k x 4k at 0.7 A/px likely will have too much gold, other camera configurations may not).