@Rok
I am not sure to completely understand, but I believe you are interested in the 3D model in which you could navigate. Our software is able to generated such a model with colors (step 2. Point Cloud and Mesh) after the initial processing of the images. In this case, the acquisition plan that I would recommend is the double grid over the area of interest. If you need more information about the different missions, check this article.
@Colin
Pix4Dcapture automatically set the image resolution to full meaning 4000x3000 (4:3) 12 MP. You cannot change this option, as we always recommend to process full resolution images to generate optimal results and get the most precise reconstruction.
About flying Pix4Dcapture with the Phantom 4 Advanced, you can provide maybe more information about you proceeded in this community thread.