Well, to answer the first part:
What I do is first, rinse everything out in the sink. Then I will use a vinager and water solution and let that sit in the rad for about half an hour. Then rinse it out. Then I will put everything together (usually over the sink) and using a bucket as a res, I will run the loop for a a few hours. I do this so any particles or debris in the loop will collect in the bucket.
Then I do the usual assembly and leak testing.
As for the second part. You need to bleed your system. The simple method of this is to uncap your T line. And cycle your pump. Turn it on for a secodn or too, then stop it. Let some of the bubble go out, and repeat until you get all the big bubble out. Then let the system run until all the "micro bubbles" are out. If you have a REALLY powerful pump you might try retarding the pumps power, you can do this by crimping down part of the tubing, or turning down the voltage on the pump (if you have it hooked up to a fan controler or similar device). This will slow the coolant flow and bleed the system quicker.