I have a sata cable from the 3 drives and then the CD burner. I also have one Sata coming from the front panel, which I assume is for firewire? I have a sata power connector plugged in to each of them. One of them is a 4-Pin Molex to Sata adapter, because the one sata power wasn't in a convenient place.
My questions are as follows:
1.) If I don't plug in 3 connectors on the cable and just use the end one, is that okay? Basically, you dont need to use them in order?
2.) I have the (20+4)pin connector for power going into the motherboard. I understand there's ANOTHER small 4 pin connector for power. Does this HAVE to be plugged in? I hear it's a CPU power supply, but the instructions on the Gigabyte board say the (20+4)pin connector will power the whole board?
3.) The 4-pin molex connectors... all of the fans for this case have both a male AND female connector... can I plug them into the PSU's 4-pin connectors either way? Meaning do the 4-pin connectors from the PSU HAVE to plug into the female part of the fans 4-pin connector? Can I "stack" them, so to speak? Like plug one male into the female of plug 2. Plug 2 male into female of 3. Plug 3 male into female of 4, etc.
You're using the term "SATA cable" for two or three different things here, so let's be sure we are talking about the same things. First, there are SATA power supply connectors that are part of the wires that come out of the PSU. Yes, there may be several connectors all on one set of PSU wires, and it does NOT matter which one(s) you use - they are all just parallel outputs to devices. Second, there are SATA data cables. These are 7-wire flat ribbons generally, with only two connectors on them. One end goes to the mobo SATA controller pinout connector, and the other end to the SATA device's data connector. Each such cable can only connect one drive to the mobo. Third, there is a special type of SATA system called eSATA, and I see that your case has one eSATA port on the front panel. Fourth, there are cables for other devices and connection schemes that are NOT SATA. For example, you say there appears to be a SATA cable of some sort coming from the front panel. It may be the eSATA cable, or it could be something else, so let's take the time to identify and connect it properly.
There are five possible cables from a front panel to connect to your mobo. One is often labeled the "Front Panel Connector" and it carries wires for the on/off and Reset pushbuttons, the indicator LED's, etc. This connects to one pinout at the bottom right on your mobo. In many cases this cable has not just one multi-pin connector on its end, but several small ones that you individually connect to the correct pins on the mobo connector.
There could be a cable for the front-panel USB connectors - your case should have this. There could be a VERY similar cable for a Firewire (IEEE 1394a) port - your case does not have this one, I think. BUT here's an alert! The connectors on cable ends from the front panel for USB and IEEE1394 ports look identical (poor design), and yet the electrical connections are quite different so that you could damage your hardware by plugging a cable into the wrong mobo connector. So in your case with ONLY a USB cable from the front panel, make sure you identify on the mobo the USB connector pinout and plug it into that. Do NOT plug it into the Firewire (IEEE 1394a) mobo port if it has one. (On closer examination of the manual, it appears your mobo does not have a firewire port, so no danger of confusion.)
There often is a cable for front-panel sound ports (mic and earphones, usually) that must connect to an appropriate mobo pinout for front panel sound. If you have this, read the mobo manual page 27 and page 105 carefully about the ways that front panel sound can be configured - there may be two options in BIOS and you need to choose, although the physical connection of the cable is the same either way.
Your case appears to have a front panel eSATA port, so there will be a cable for that and I assume that is the one you mentioned in your post. From your mobo manual it appears it has no dedicated eSATA controller, so we have to assume all the required eSATA features are provided in the regular SATA ports numbered 0 through 5. (Ports 6 and 7 are specifically for new SATA 6GB/s.) So I guess your front-panel eSATA connector has to go to one of those ports 0-5.
Re your item #2 on power connectors, I looked at your mobo manual, see its page 22. In your case you have a main (20+4) pin power connector that goes to the long 24-pin input at the top right of the mobo. You may have to remove a plastic cover on the last 4 pins to make the connection. There also will be a 4-pin 12 VDC ATX power connector on wires from the PSU to supply power directly to the CPU. On the mobo there is a 8-pin connector for this at the top left. But of those, 4 pins are covered by a plastic top. Those four pins are only used if you have a different PSU with an 8-pin output for here. In your case leave the cover on and plug your 4-pin power connector into the exposed 4-pin socket on the mobo.