You need a bucket which can be crafted. Then fill it with water at a well or river by having it in your hand and (right?) clicking. Then using the filtration unit, get a bucket of clean water, which you can then finally put in the ditch by (right?) clicking with it in your hand while pointed into the ditch.
One bucket will also fill 4m of ditch, if I remember correctly.
Okay, quick question. Went to download 5.5 with the mod launcher, and it's syncing 5.4? (https://gitlab.com/jaxteller718/rh_5_4_17_4_client.git) Is it actually the new file, just reusing the old name?
Update: Yes, just tried it. It is 5.5 just using the old filename.