im guessing the other drive is IDE or EIDE.
I.I.W.Y. I would firstly back up all data to DVD-RW or DVD-R for a safety measure.
This guarantees any data loss if your new to this kind of thing.
Remove the E / IDE drive from your machine and allow windows CD to partition and install the operating system on the SATA. this also prevents any formatting of the drive with the original data if your not sure.
Usually port 0 is good as primary from your bios for your sata
Once your OS is running on the faster drive anyway, the whole system will behave better.
Your IDE drive will suffice as a temp drive back up space once you start using SATA as your primary. If i were you at this stage and have the means to get another SATA, set up a RAID.
this way your twin SATA RAID level 0 config allows you to store data on the hard drive with more confidence then one copy of the data on one drive.
It also heavily depends on your motherboard, so I can only give you the basic premise to your problem.