To process your own images it is valuable to have a look at the way the test images have been processed by the script process.csh.  First it is good to create another directory and to make a copy of all the files in register there.  You will have to modify the configuration files to give the paths for the different files, and set correct the parameters for the set of programs. See the next chapter for more details about the configuration files. Let's now give some idea of what are the basic operations performed by process.csh:

Registration and interpolation of the images: script interp.csh

Stacking of images to make a reference: package stack

Getting accurate coordinates for the variables: image subtraction+package stack

Image subtraction+photometry: script phot.csh

Display the file process.csh to see the detailed list of commands, your own process script should look like that, have a look at the rest of the documentation to see how to set the various parameters in the configuration files.