Starting out with 3ppm ammonia is fine, it is probably more than you will need for the stock that is appropriate for a 29g, but starting there will not slow things down all that much. What will slow you down is if you add ammonia to often or dose too high when it's time to add more. When the ammonia finally gets to 0ppm I would only dose it back to 1ppm. Have you tested for nitrates yet? If there are nitrates, then there was a nitrite stage and it was either very quick (unlikely), or in very small amounts. It's even possible that the nitrite converting bacteria grew in larger quantities than the ammonia converting bacteria, but this usually happens when you seed the filter with media from another filter.
For the filter question, it is preferable that you leave the HOB alone and let it cycle, but if it bothers you too much you should be able take the media out of it and put it in the canister filter without disturbing the cycle too much. Make the switch quickly and don't let the HOB media dry out.