AIO skimmer

[Keto_Reefer]

Looking for opinions on where to put the protein skimmer in the back chambers of my jbj-45.  Recently  got an eshoppes nano protein skimmer an originally put it in the second chamber on the right.   In that spot the magnet had to be in the water of the middle chamber so i put it in a ziplock.   It was not the easiest spot to then take out and empty the cup every couple of days so i removed the media basket on the right side and that way the magnet can be outside of the tank on the rear wall.

 

Will doing this not provide me with as much benefit since I removed one of the two media baskets or should it be alright?  Never used a protein skimmer before so this is my first experience.   My tank has been running almost a year and just now added a couple of coral frags, of zoas and a sun coral.

 

Thanks

[Keto_Reefer]

Another question for those with an AIO, with the two media baskets in the back of my system what would be the difference in using a reactor with GFO and Carbon then just putting GFO and Carbon in a fine mesh nylon bag in my media baskets?