Question : Problem: What issues might I face by installing an SATAII Controller to a Dell PowerEdge 2600/533?

I will be switching our 74GB 3-drive SCSI RAID5 system to a 320GB 3-drive SATAII RAID5 w/hot spare on our PowerEdge 2600 server.  
I have researched and there doesnt seem to be a whole lot of hardware specific information about doing this.
I have setup/maintained RAID0/1/5 on new systems that I have built myself, but have never done an upgrade like this.

I am looking at this card:
 http://www.newegg.com/product/product.aspx?item=N82E16816131001
with additional battery backup:
http://www.newegg.com/Product/Product.aspx?Item=N82E16816151019
 $$ is pretty much set in stone, so if another card is recommended please keep it somewhat in that price range

I will be cloning the existing SCSI drives to the new SATA.
I want to make sure that I can boot from the new drives connected to the new controller.

Any tips for the noob?

Answer : Problem: What issues might I face by installing an SATAII Controller to a Dell PowerEdge 2600/533?

Here is your system specs:
http://support.dell.com/support/edocs/systems/pe2600/en/sm/intro.htm#wp1046321
More infor:
http://support.dell.com/support/edocs/systems/pe2600/en/sm/remove.htm#1101771

From what I see, you will install sata card (PCI/PCI-X type). So, make sure you have right type.

From your comments above, I would suggest, you install the sata card but not remove the scsi. Then, if you have imaging software (norton or acronis, or else) to image / clone the whole to new sata. This will save you a lot of time to reconfigure later.