Not certain exactly what you mean by the bottom is 4 and the top is 2. The liguid in the tube should be the same color through out. As for how long it will take and whether you need to add more ammonia, if you haven't already read it, check the link in my signature about fishless cycling. It should give you all the info you need.
As for the test kit, I hold the card straight up with the tube beside it in normal light. I have never had any problem distinguishing the colors except as previously mentioned with the nitrates.
The key thing to remember here is that you really should have a 0 reading for both ammonia and nitrite. If you are getting anything else and your not in the process of a fishless cycle, regardless if it looks like .25 or .5 or whatever, then you have a problem and need to do water changes to reduce the toxins.