I'm not familiar with your Roo but, yes, most of it can be done connected via the city water line.
Just run everything until the water is no longer pink. If you have a re-connect switch on the water pump, hook up the input hose and run some clean water through the water pump. Then, switch it back to run from water out of the fresh water tank.
The final step is to prep the water heater by installing the drain plug then switching the bypass valves to normal use. (I'll flush out the water tank at this point, too, as a small amount of pink stuff might have been in the line and don't want that in the tank.)
Oh a second final step (!) will be to disconnect the water filter holder (which should be thoroughly flushed at this point) and insert the water filter.
At some point, you're also going to want to disinfect all of the lines by just running some water with a little household bleach but those instructions are already posted in detail here.
Rick & Karen
(Retired USAF, MSgt)
5-year Travel Trailer RVers
2013 Forest River Rockwood Ultra-Lite 2904SS
2014 Toyota Tundra Maxcrew SR-5 TRD 4x4