Help with filter/skimmer 37gal...please

Hi all. As usual I'm confused. Currently I have a 37 gal. with an
eclpise hood/filter and about 25 pounds live rock. The inhabitants
are a longhorn cowfish and a thornback (helmet, hoovercraft) cowfish.
The nitrate/nitrites have been high and recently my longhorn has
developed a fungus on his eyes. I am treating that with eye fungex
drops. I think I should get a protein skimmer however you can not
hang one on the eclipse hood system. So, I am going to replace the
hood and also buy a new filter. My LFS recomended the Bak Pak system
with the filter and skimmer all in one unit. Is this the way to go or
should I get a seperate filter and skimmer. If seperate, which do you
recomend? Is it better to spend the money on a better skimmer than
filter, or vice verca? Or are they equally important? I am kinda
hoping the you recomend the Bak Pak. It seems like an easy unit, but
I have been burned before choosing style over substance (Ecllipse
hood/filter/light). I hope to do this this weekend so lets hear what
everyone thinks.

Thanks
Phil

PS
It's really weird holding you fish in your have and putting in eye
drops. However he took it well. I think we bonded a liilte.