Installing a Biocube Protein Skimmer??

Hello! I'm trying to install a BioCube Protein Skimmer for a 29 gallon tank. The instructions said to remove the filter cartridge. If I do that, won't it adversely affect my natural bio filtration? If I leave it in there, how can I make it fit with the protein skimmer and heater all in the same first chamber? 

I pushed the filter cartridge up against the overflow wall between chambers 1 and 2 and then hung the protein skimmer on it. I'm just not sure if the protein skimmer is submersed in the water enough because even though I have the air valve open all of the way there doesn't seem to be enough foam/bubbles coming up to the top of the reaction chamber. The water level in the aquarium is already above the maximum level. 

What should I do in this situation? 

Thanks in advance for any help you can provide!! :)

It's a Biocube Protien Skimmer, I finally was able to get more bubbles/foam going, but I'm not sure if its enough. Should I turn the air valve higher? I've included some pictures below...

arrrrrrgh!! The skimmer still doesn't seem to be working! It's been in there for about a week now. The foam doesn't come anywhere near the top of the little plastic cup. I opened the valve all the way and that didn't help. I took the skimmer out and checked that every tube was snugly in place and still it doesn't produce that much foam. Is that because the aquarium is only 2.5 months old and I have a low bio-load, or perhaps because the skimmer has only been in there a week? I have gotten a little water collect in the collection cup...but not much. How should the water that collects in there look? 

hello! 

Everything is going well so far, Spanko is a genius when it comes to aquariums! I'm still a rookie when it comes to SW and my tank is new (about 6 months). I haven't seemed to have a lot of the common water quality problems. I can only attribute that to the wonderful advice that people on this sight have given me. As far as how I ended up adjusting the filtration in the back here's what I've done:

In the far right chamber I have the heater, and BioCube Protein Skimmer hanging on the little plastic wall (the same place where the instructions had suggested I place it). I'm not really sure how well the skimmer is working, because honestly I have such a low bioload right now that I might not actually need it. I do get some yellow-ish water in the plastic container every once in a while. I change the wooden air stone of the skimmer once a month. I realized that I can purchase two wooden air stones (made by Red Sea I think?) for less than the price of 1 BioCube wooden air stone. When I take out the old air stone it's completely black and is covered in slimy stuff. *I took out the stock carbon filter that came with the BioCube, it really wasn't necessary. Taking out the stock carbon filter really helped everything else fit well in that chamber.

In the middle chamber I have the bioballs that came with the cube (I did take out a few handfuls of the balls and throw them away to make room for other types of filtration). On top of the bioballs I have one bag of Chemi-Pure Elite and one bag of Purigen. I honestly don't know what either one does, however Spanko suggested that I put them in there and so far my water quality is great! On top of the Chemi-Pure and Purigen I have the plastic 'overflow tray' and laying on top of the overflow tray I have a piece of carbon filter pad (the type that you can cut in order to get the size you want). I also have some filter floss (about the size of a pickle) sitting wedged up against the right side of the middle chamber (where the water flows from the right chamber to the middle chamber). I change the filter floss every other day or sometimes every 3 days (basically when it's starting to look kind of brownish and dirty). 

In the left chamber I only have the blue sponge at the bottom (the one that came with the Biocube). 

If you have any questions, please don't hesitate to ask!

I definitely noticed an increase in water flow when I removed the stock filter. The Chemi-Pure and Purigen are both completely submersed in the water (it doesn't look like it in the pictures below, but that was before I took out some of the bio-balls). After I took out some of the balls, everything except for the sponge part of a filter sponge (in case I need to set up a QT or hospital tank) is totally submersed.

Here are some pictures of how I set up the filtration step by step...(it's been working so far, hopefully it will continue to do so after I add a little coral and another fish or two in the following months) If you have any ideas on how I can improve it please let me know. I really appreciate advice and feedback!

This is the middle chamber and left side chamber. 1st, (in the middle chamber) I have some bio-balls and on top of the bio-balls I have 1 Unit (bag) of Chemi-Pure Elite. 

2nd,I  I placed a bag of Purigen on top of the bag of Chemi-Pure. I also keep the sponge part of a simple sponge filter in the middle chamber (to grow good nitrifying bacteria), so that it can be used in a QT or hospital tank if needed. 

3rd, I place the plastic over-flow tray on the top, and then a piece of carbon filter pad on top of the over-flow tray. Lastly, I wedge some filter floss against the side where the water flows from the first chamber to the middle chamber. The filter floss fits on top of the carbon filter pad and under the Protein Skimmer. 

In the first chamber I have a heater and the protein skimmer.

Yep! gojosie1 is is correct. It's the white mesh bag that the Chemi-Pure comes in. The photograph definitely makes it look like a plastic bag though :) 

By the way, what do you think of the filtration system? Any suggestions? 

That sounds like a great idea! Do you think the protein skimmer will still fit hanging on a lower wall? What would you suggest that I use to cut the plastic?