As 3D culture systems are still at infancy, I doubt that there are no any standardised protocols in public domain till now. Based on my experience with agarose gel, you need to first lay the gel in culture plate wells and then seed your cells on that gel. This way you will get better results as compared to embedding the cells in gel (mixing volume of gel and cells and then solidifying it). For colony formation, once you get your cell growth standardized, you can put 5,000 cells in one well (resuspend them in 1-2ml culture media) and then allow them to grow for 7 days and photograph once visible colonies are formed. You can also do temporal photography of cells on each day to get a real time insight.