thmt,
Welcome to the forum!
I think your problem may have come from the new filter, however I dont think the issue is with the filter itself but rather the loss of the old filter.
First, if you are not familiar with the ins and outs of a cycled fish tank, take a look at these two 'sticky' articles:
http://www.fishtankforums.com/5-fres...-aquarium.html http://www.fishtankforums.com/5-fres...cycle-how.html
These bits of information will key you in to how bacteria in your tank is going to keep things healthy for your fish.
From most of the typical methods of keeping betta fish that I have observed since getting into this hobby, I have noticed that most times they are kept in tanks or bowls with very small amounts of substrate and decorations. While I could go on forever about my opinions on doing so, small amounts of substrate and decor results in having less space for benificial bacteria to grow in these vessels and so most often the filter media is where the bacteria is found in its highest concentrations. Since you just changed filters and assuming that you did not use the old filter media in the new filter, I would take an educated guess here and say that I think your fish may be suffering from ammonia or nitrite poisoning right now. Depending on how long your old filter media has been out of water, it may or may not pay to try to put it back in the new filter.
The good news is that you are using a filter here which, again from my personal observations, most people do not do. I am sure that you are well on your way to cycling your tank again, but in the mean time, you may want to do a quick 50% water change and then go pick yourself up a test kit that will allow you to monitor the ammonia, nitrIte, and nitrAte levels in the water. This way you will be able to keep an eye on each water parameter and act accordingly to help your fish stay alive. Since ammonia and nitrites are toxic to fish in relatively low amounts, it is important to keep them down to low levels while your bacteria colonies grow so that they can do the work for you and your fish. NitrAtes are also toxic to your fish, however only in larger amounts and so water changes on a regular basis can usually keep the nitrate levels low enough to not impact anything negatively.
I hope this can help you a little bit or at least start a more in-depth conversation about your particular situation.
Betta Blues 
I don't know if I should seclude him in his own bowl or what. He was thriving well and since the new filter not so well. Any help would be good. He doesn't have any spots or anything like that, I just want to do what is best for him. 
