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What should be the best practice for a merged project with different altitudes ?

I have to survey a terrain, with different elevations (the maximum difference in altitude is ablout 100 m). I will be flying an UAV at 150 m and another at altitude of 200 m. Which kind of practice should I follow and what points should I consider while surveying ?  Is their any role of GCPs ? (All the elevations are from same reference level.)

If you have the ability to take some GCP’s, that would make things a lot easier for you.

I flew a 2 km square project from a couple different elevations, when i merged the projects it was a complete jumbled mess. I added my GCP’s and that helped a bit, but the true magic came from adding MTP’s

Once those were added it was perfect.