We will come back to the speaker after the other points have been addressed.
Next, I'm not sure how to set up the computer after all the parts are installed.
The first thing you must do is format the HDD and install the operating system then the MB drivers, to do this you must change the boot sequence in the BIOS to DVD drive first and the HDD second, see details below;
To change Boot Sequence in your BIOS;
Reboot the system and at the first post screen (where it is counting up memory) start tapping the appropriate button that allows you to access the BIOS (Del – F8 etc)
This will enter you into the BIOS/CMOS
Find the Advanced area and click Enter
Look for Boot Sequence or Boot Options and highlight that click Enter
Now highlight the first drive and follow the directions on the bottom of the screen on how to modify it and change it to DVD/ CD drive
Change the second drive to the C or Main Drive
Once that is done then click F10 to Save and Exit
You will prompted to enter Y to verify Save and Exit.
Click Y and the system will now reboot with the new settings.
While you are in the BIOS you will also need to reset the time and date and again save the new settings (F10) and then Y to accept the changes.
I only have two drives, so one connector is doing nothing. Is that okay.
Yes that is fine just make sure that the cable is tucked away securely.
I also connected the gpu via psu cables, instead of the ones that came with the card, because they had ends on them I couldn't connect to the psu. It is a 660Ti
The cables that came with the video card should be the PSU 4 pin molex type to the PCI-E type that the video card requires.
and I don't know if I need both power cords or just one.
Both power cords must be connected to the video card.