The answers to these questions really depend on which internal parasites you're targeting.
Metronidazole is indicated for protozoal infections; whereas piperazine is indicated for nematode (aka roundworm) infections.
Metronidazole can be mixed with the food (see below), as can piperazine. I am not sure what dose rate you would use for piperazine, but Gratzek & Blasiola (1992) suggest an incorporation rate (in feed) of 0.25%. I'm not sure I would add either to the water for treating an internal infection - mainly because I doubt you would achieve therapeutic serum concentrations. Keep in mind that while metronidazole has a very wide safety margin. I doubt the same is true for piperazine, which is a neurotoxin. Can't say much else regarding piperazine as I've never used it.
I have used metronidazole for the treatment of external protozoans. However, I can't say however effective the drug was. When used in conjunction with other options (used of cleaner shrimp and UV) it seemed to help. I do note that it did very little when added to the water as the infection I was dealing with seemed to get cyclically worse. However, formulation can play a big role as some incorporate carriers, which may facility uptake by the tissues. Nonetheless, I did suspect that the in-water treatment affected my biological filter as my water parameters (ammonia/nitrate) shot up shortly after a long treatment course at a very high dose. I then switch to an in-feed treatment using an incorporation rate of 250mg/100 g of feed. I made the medicated feed myself using fresh/frozen stuff in a blender with gelatine, and then froze it. I fed this 2x/day for 8 days. Like I said, I feel it helped but it's very difficult to say with any certainly. At least the fish tolerated it very well.
Not sure I would mix the two - mainly due to a lack of knowledge on possible negative interactions.
Not sure if this answers all your questions. Can't stress enough though that I would start with a clear (or as best as you can get) diagnosis before considering treatment options. Not doing so is essentially a waste of time, money and will only delay initiating the proper treatment/course of action.
Hope this helps.