The resonator box is a thing that attaches to the intake pipe, and has no particular purpose. It doesn't change the sound of the engine in any way that I can see. If you look on top of the engine from the back on the passenger's side of the engine there will be a black, roughly square, 4" thick, 12" wide black box that attaches to the intake pipe with a hose clamp. It's a pain to get at the clamp, that is why it is popular (and fun) to just smash it to bits to get it out. It is really hard to get it out of there with all the stuff on top of the engine. That is also another reason to remove it abortion style.
About the filter bowl, don't fill it with anything, just start cranking the engine, and it will fill by it's self. One thing I like to do on the older trucks (97 and older) is to get the engine warmed up for a few minutes before I change the filter. That way you only have to deal with the fuel shortage instead of a cold engine that doesn't want to start and
a fuel shortage. That engine doesn't have an electric fuel pump, so priming it just means cranking it.
The reason why you don't want to fill the bowl before you put a filter in it is because the bowl is probably really filthy. If you fill the bowl with no filter in it, the "clean side" will get debris in it from the dirty side.
At some point you may want to remove the fuel bowl and clean it. Every one that I have removed has been horribly dirty. While you are there, you can replace all the o-rings in the bowl. It will help prevent future leaks. www.dieselorings.net
has everything you need at really reasonable prices.