It sounds like you fried something on the motherboard. Is it something critical? Don't know.
First problem is to get the motherboard to POST. Find the motherboard manual.
Do not do anything until you find the motherboard manual.
Disconnect all the wiring from the motherboard except the two power cables and the case power switch and the case speaker.
The following is a cut & paste of a previous reply. Ignore everything that does not apply.
Disconnect
everything from the motherboard except the CPU and HSF, the two power cables going to the motherboard,and case power switch.
Boot. You should hear a series of long single beeps indicating missing memory. Silence here indicates, in probable order, a bad PSU, motherboard, or CPU - or a bad installation where something is shorting and shutting down the PSU.
In your case, a totally fried motherboard.
You should not need to pull the motherboard, but it will make troubleshooting easier.
To eliminate the possiblility of a bad installation where something is shorting and shutting down the PSU, you will need to pull the motherboard out of the case and reassemble the components on an insulated surface. This is called "breadboarding" - from the 1920's homebrew radio days. I always breadboard a new or recycled build. It lets me test components before I go through the trouble of installing them in a case.
It will look something like this:
http://www.tomshardware.co.uk/forum/page-262730_13_0.html
You can turn on the PC by shorting the two pins that the case power switch goes on.
If you get the long beeps, add a stick of RAM. Boot. The beep pattern should change to one long and two or three short beeps. Silence indicates that the RAM is shorting out the PSU (very rare). Long single beeps indicates that the BIOS does not recognize the presence of the RAM.
If you get the one long and two or three short beeps, test the rest of the RAM. If good, install the video card and any needed power cables and plug in the monitor. If the video card is good, the system should successfully POST (one short beep, usually) and you will see the boot screen and messages.
If you make it this far, you have not fried anything really critical. hook up the monitor, keyboard, and mouse. System should boot and display a "Missing boot device" message on the monitor.
Now, to answer the thread title:
"Does it matter ..."
Yes ... and no. If you plug the C: drive into any other than the first SATA port, you will need to go into the BIOS and adjust the boot order of the hard drives. If you plug the drive into the first SATA port (SATA0, usually), the BIOS will automagically find the boot drive.
If you get this far, start connecting the rest of the case wiring, stopping to test after each one.
And next time, before you do any work inside a case, RTFM and pay attention to what you are doing.
I have been doing this for a few years. Anytime I am going to poke around inside a case for any reason, I always have the appropriate manuals on hand. And I always keep detailed notes in a maintenance log. Takes time because I usually have three computers tied to a 4 port KVM switch.
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Building computers since 1977.