ArtPog :
First of all since it appears that you've apparently had no experience in this area it really would be desirable if you could arrange to have someone reasonably experienced at your side as you make these connections. The process isn't difficult but you're dealing with pretty sensitive electronic equipment and things can go awry if you don't really know what you're doing.
Anyway, with that as a caveat...
1. Connect your SSD to the motherboard's first SATA connector which will either be designated SATA 0 or SATA 1 depending upon the particular motherboard. In all probability the present 1 TB HDD in the machine is connected to that connector so it would be necessary to uninstall that disk from the connector.
2. Assuming that you would plan to utilize the 1 TB HDD as your chief secondary drive - connect it to the second SATA connector.
3. Connect your final HDD to one of the vacant SATA connectors.
I'm assuming in all this that the motherboard contains at least 4 SATA connectors to accommodate your disk drives + optical drive. Most likely the MB will contain more than 4 SATA connectors so there shouldn't be a problem there.
BTW, judging from the specs on Newegg it certainly appears to be a fine PC for the money although I was a bit concerned with the fair amount of negative user reviews. Was $799 what you paid? Any idea of the make & model of the desktop's motherboard?
Hi there. Thanks for your reply. My motherboard is an ASRock 797 Anniversary (http://www.newegg.com/Product/Product.aspx?Item=N82E16813157528). It has 6 SATA connectors starting with SATA 0, which like you said is more than enough to cover everything. As for the computer itself, I did pay the $799 for it. I too was a bit concerned about the reviews, but so far things have been going well. The only issues I've had with it at this point have been a missing screw from one of the sliding side panels and lag spikes with the wireless usb. But I'm getting a PCI wireless adapter to replace the usb.
The old HDD I have is a 2TB 7200rpm drive (http://www.newegg.com/Product/Product.aspx?Item=N82E16822148834&cm_re=seagate_barracuda_2_tb-_-22-148-834-_-Product) while the new one is 1TB 7200rpm so I'm not sure whether or not I should make the old drive the chief secondary drive or not. The old one does currently have some files and programs on it that I'd like to still have access to. I'm not sure how much this all matters though since on my old computer I had only really ever used up about 500gb between my two drives and will probably still stay somewhere around that range.
If there is more I need to do beyond just hooking the drives up to the SATA connectors/power supply for my situation, (such as formatting, configuration, or doing stuff with BIOS/boot) it'd be great to get a detailed step-by-step.