This is a good thread and it is helpful to my own setup ideas.
As I was reading along, my personal recommendation was precisely what Joann (aka CliffandJoann) recommended - basically looping the two ponds together so that they will work together as one larger pond. I thought that this would be a fine idea for the bacteria culture thing and "kick-starting" the new, smaller pond.
However, as Waterbug stated, you would want to wait out a quarantine period, (isolation period) before moving the new Koi fish to the larger pond. Now, it is this part of it has me thinking. When you get into Koi fish, how much isolation and quarantine is required before you introduce the new fish to your main pond? Are there many parasites and diseases that could be transferred between the fishes? If you loop the two ponds together to make it basically one slightly larger pond, wouldn't sharing the water system defeat the purpose of the quarantine excercise?
I am raising this concern because I was pondering about doing a similar thing (sharing the same filtration and circulation system between two tanks). I say "tanks" in my case because I don't actually have a pond, I have two approx 1,000 gallon polyethylene tanks. My original plan was to just keep live fishing bait in them, but have been pondering raising Koi in one of them to sell in order to help make up for a small bit of the expenses for maintaining the system. However, I am now concerned that this might be a bad idea and a bad practice. My bait fish could transfer dieseases and parasites to the Koi, if the filtration system didn't isolate them sufficiently.
I can build a second, mirror system for my purposes and elliminate this problem (although it would be less expensive to share the filtration and water conditioning / circulation systems).
For your situation, Likoi, would connecting your two ponds together be asking for trouble when you get new fish in? If you were intending to use the smaller pond as an isolation center, I would be concerned that you may not have a true isolation system if you did this. Of course, if you did so, you would only risking your own Koi. However, for what I was planning, it might be an extremely poor practice. People who are in the "know" probably wouldn't want to buy my Koi if they knew that I shared a water conditioning system between the Koi tank and the bait-fish tank. They would risk their existing Koi stock being exposed to who knows what kind of parasites or diseases from the bait-fish and I certainly would NOT sell any Koi that I raised in this fashion to anyone who were concerned for their existing Koi if there could be a possible threat. We're not only talking money in this case, we're talking about, in most cases, someone's pets that they are very attached to.
Likoi, does my logic here make sense in regards to the isolation or quarantine issue for your setup? If anyone else can add input, that would be beneficial, but I think that you were intending to utilize the smaller pond as sort of a quarantine area in this case, if I understood you correctly.
I guess what I am asking everyone and what I am elluding to is... How much isolation and quarantine is necessary for Koi fish when you buy new ones or raise them to be sold to others for their ponds? What I have been digesting by reading here and other places is that Koi are very sensitive fish, to their environmental conditions, water quality, and to diseases, etc.
Is this correct? Or is it not quite that critical?
Gordy