After reading some of the posts on here I have discovered I need a bigger better filter. From what I have read the good bacteria that you acquire in your tank lives in the filter.
I have a top fin 30 and I'll be getting a top fin 40, I have a 20 gal tank and have figured out I need at least 200 gph. I would be getting a better quality filter but I lack the funds right now.
Anyway, my question is this, with the good bacteria in my current filter how bad is it going to screw with my tank to put a new filter in? Any advice would be greatly appreciated!

What I did when I got my new Penguins was take the bio-pad from my old filter and put it in the new filter. That way, I didn't lose any BB's that were on that filter pad.
Most of the Bb's do live in the filter, but they also cling to any surface in the tank, like the sides, the top layer of gravel or on river pebbles, and ornaments. Does the Top Finn have room in it to put the old filter pad in with the new pad that comes with the filter?
Or, do you have room to run both filters at the same time?

Also, I don't think I am telling you the wrong info here, but I want to apologize in advance if someone states I am wrong, as it does happen alot!

I had a Top Fin 30 that came with my 28 gal tank. I also added a filter. Since you are getting another filter, I'd recommend the one that I got...a AquaClear 50 (200 gph). You should be able to pick one up for under $30. You can run both until the new filter is cycled.

AquaClear's are much easier to maintain. It uses a sponge filter and some type of ceramic bio balls. The sponge and bio balls can be rinsed in the water from a water change. The sponge will hold up much better than than Top Fin's filter.