Thanks for your interest in Pix4D software solutions. I understand how frustrating it can be to get up to speed on how to create accurate photogrammetry deliverables.
1. There is no “Set” minimum distance between two GCP points. You need to take into account your project Ground Sampling Distance, the required level of Accuracy for the project and the local terrain variability. Typically I would suggest having a GCP ~500 feet, but this distance may not be ideal for every project.
2. Pix4D offers a number of support articles on how to implement GCP’s a couple of good ones to reference are:
How to add / import GCPs in the GCP/MTP Manager & Using GCPs
3. The GCP data you wish to use for a project must be visible in multiple photos of that project. If you have sub projects without GCP points being shown, these sub projects will need to be merged into data that has the GCP data visible in it.
I also encourage you to participate in aPix4D User Workshop. These 2 day user workshops really help new users establish efficient work flows to achieve the best results.