In theory, you just use which ever one you need at a particular location be cause you're supposed to be able to mix and match the MPRotators 1000, 2000, and 3000 because of the matched precipitation rates.
Obviously, where you can, you try to use 3000 just so you don't have to install as many heads.
But of course there can be all sorts of overriding factors. You should be designing to a particular expected flow rate per circuit, and therefore you have to make sure your choise of heads can support the required flow rate. However, changes in pressure at various heads can make this job difficult.
Personally, the thing I did with the MPRotators was to design it such that each head should have plenty of pressure (like 45psi) and then to better match all the heads, used the 30PSI pressure regulators (RB1800PRS).
In the end, there is no wrong way to do it so long as your flow rates and pressure losses can support the spray pattern you expect at the spray head.