You are missing nothing - the manual is very poor.
On both my NH TC40D and RK55, the procedure has been to close off the fuel supply valve, remove and clean the bowl, clean/check and/or replace the filter element, reinstall the bowl, reopen the fuel supply valve, and bleed the fuel system - all easy stuff except bleeding air out of the downstream fuel lines. It was easy on the NH - one bolt on a "banjo fitting". It was more difficult on my RK55 mostly due to the terrible translation of instructions in the manual, but there is a bleed screw on the filter housing (the RK55H has both a fuel filter and a separator). I'm not sure of the procedure on the RK24, but it SHOULD be similar.
I looked at your owner's manual on line and saw no instructions on HOW to bleed the system. In fact, the picture on 5-13 on section "FUEL" has something labelled "filler cock", but the text refers to "filter cock"; the identical text is copied-and-pasted on page 5-14 on section "CLEANING OIL WATER SEPARATOR". Page 5-30 has 3 points about the "FUEL SYSTEM". But that's it - very little help.
So you are correct: per usual, the owner's manuals are horrible. Perhaps if you look at pages 5-12 and 5-16 of the RK55H manual online, you can get a general idea of how to do it.
Before you do this service, I have to ask the question - do you even need to clean the separator? Both bowls on mine are clear enough that I can see any water on the bottom (oil floats, water sinks) and can see how dirty the filter element is.