Most ponds really take one or two years before they settle in. Those first few years, algae blooms are normal and to be expected. As long as the water is filtered and aerated, the fish should be fine. I would be more worried if a new pond didn't have an algae bloom. That would mean either there's not enough light, or the water is not even good enough to grow algae (not a good sign). My 1800 gallon pond is now 11 years old and hasn't had a real suspended algae bloom for probably 7 or 8 years. I'll get transient minor blooms for a day or two usually when the goldfish spawn and make a huge mess.
The actual nitrogen cycle in a pond that's stocked will take a few months to get through. If you stock lightly and build from there, you'll never have readable ammonia or nitrite ever (I never did or have).
I've never built a Skippy filter myself but many have had good look. Like Frogman3 said though, the filter does need regular cleaning like any filter to work well. I've also never used quilt batting.
My algae page at
http://www.fishpondinfo.com/plants/algae2.htm lists ways to control algae. Basically, lots of plants, good filtration, lots of plants, some shade if needed, good bacteria, perhaps some barley straw, and, did I mention, lots of plants?
Good luck with your new pond project!