I mean, if you are in Corel or Photoshop, you can send over all the separated colors or each one individually. If you do all of them at once, then you should use the "lock screen" function since each color will come in, rip, and print. If you send just the C, Y, M, or K, or any other color, then it will come in as a separate file (color) and will rip individually, so you can set each screen's output as a separate input for each color before it comes in. After that color rips, change the settings & send over the next color, and so on until all the desired films are printed.
For example, let's say you are doing a simulated process print. If you use Separation Studio, it will save it as a .dsc2.0 file which is a form of a .eps file. It saves each color layer in one file for separation output. If this is put onto a template in Corel, you would then go to print the file. In the print menu you can select the separation colors individually or send all the colors over. Same thing as with CMYK. The settings in Accurip will override any angle and frequency setting in this menu, which is why you need to choose how you need to send each color or all colors at once.
All at once = all screens print the same angle and frequency. One click, One result.
Individual = Each screen can be set at different angles or frequency. Angles between screens are adjusted rather than frequency.
The .pdf of the manual lacks a lot of information as to the potential of the software. Once you get a grasp on it, it really is worth the money for it.