[What is the best method to put my small colony into my observation hive?]
At night with a single backlight behind the Ob. hive.
Stray bees will fly towards the light and thus into the hive.
[...and close it up for a couple of days?]
It is an observation hive right?
I hope you plan to close it up.
[ What is the best method to put them into a Kenyan Top Bar? ]
Does you hive body take standard frame bars?
1. I'd rubber band the combs to frames and insert them.
2. Then I would add top bars for new combs (slowly until progress is seen).
3. I'd slowly wean out the old frames and combs.
Step 3 might be difficult this time of the year as the the hive is likely building towards winter.
you'd probably not want to disrupt that too much, else you might kill the colony.
Or, if disease or really old combs, I might shake them out onto starter strips.
In either case I would be sure to feed and even consider a pollen suppliment (if SHB is not a concern).