How you time your flights really depends upon what you’re trying to do.
Are you scouting early-season? Where I worked, we did some limited sUAS scouting, but mostly we used my sUAS surveying for making prescriptions and checking (in a few cases) trials.
How you get that prescription onto your equipment is highly dependent upon the equipment… Not only the make, but the model (and sometimes, even the firmware version ). You’ll need to know exactly what you’re putting it into to know what formats it accepts, how to write them out to the storage, and how to sideload them.
In general, yes, it is all proprietary software. You can skirt some of it and make prescriptions, fields, boundaries, guidance lines, etc. in QGIS and then load them, but reversing how they do it is time-consuming and a bit of a game of whack-a-mole. I, unfortunately, was not able to take any of my tooling with me when I left that job.
There are a number of QGIS plugins you can try, though.
If you’re looking to apply nutrients, you’ll be looking for depressed plant vigor. How you assess that depends upon your sensor and what indices are appropriate.
You can look at just gross NIR reflectance as a metric, or you can use NDVI with an appropriate sensor and look for areas of lower NDVI.
Whether or not you ground-truth it is up to you. I developed an index for our sensor (GoPro Hero4 Black + KolariVision Infrared Full-Spectrum Conversion + KolariVision Infrared Blue/NIR NDVI Filter) that was very highly correlated to leaf/ground-level NDVI, but was not equivalent because I suck at math and couldn’t figure out how to normalize it
So, once we bore out my index, we stopped ground-truthing, but again, that depends upon you.
Do you have implement-level NDVI, like GreenSeeker? If so, you might as well collect the data as you’re running over the field to spray or do other work, right?