So you want to build a koi pond, eh? Well, heres what I've gotten out of your post. You have two ponds, roughly 3000 gallons each.
You haven't added plants or fish yet, thats good. A true koi pond has only koi. Plants add to the bio load on the filtration. Although they do remove bad things like nitrates and ammonia, they only remove it in trace amounts. They oxygenate the water by day, but take oxygen at night. And when they die, they rot and become dissolved organic compounds, increasing the strain on your filters. A pond with plants is great, but not with koi.
If you want to see your koi live for more than a decade, and you want perfect water clarity, I'd suggest a maximum of 4-5 koi per pond. There is an old rule of thumb that says 250-500 gallons per koi, but that only applies to koi under 12 inches in length. Keep in mind that koi, given the proper conditions and feeding, will grow to enormous sizes, and waste production increases exponentially.
You say you have 3- 4 feet of depth, thats good. Shallow ponds have problems maintaining oxygen levels and
give predators an easy shot at your fish.
I would recommend an aerated bottom drain and a moving bed filter for each pond. You will need a surface skimmer for the lower pond.
Again, these are optimal conditions...
In order to get the best answer for you, please describe your pond system to the fullest extent. Also, give a budget.... We can point you the right way.

---Hope this helps!---
---Kenny--