Alright so this mess started when I added my SSD, What I think occured is I somehow switched which sata channel went where. The first error I get is that the RAID 1 has been degraded (not destroyed, the HDD still works it was split back into 2 Harddrives).
 
Question 1. How do I rebuild the raid array? I rebuilt an array before when the drive actualy was fried and it was like 1 click of a button, I am pressing F10 to enter raid cofniguration and press"R" to rebuild but getting nothing. I am looking for the manual to see if there are specific sata ports on the board I need to use.
 
Question 2. When I boot now, I have set the HDD to boot first but I still get the options in the following picture. IF I select the bottom option, it boots my HDD. If i select the top option it boots my SSD. Why does the computer not just boot into the one that I have set to boot first through BIOS? Also When the SSD is plugged in by itself I get the error messages in the second picture, leading me to think some part of the operating system of the SSD somehow was installed on the HDD becuase it wont work without it?  Any ideas?

 

 
Here is a picture of my motehrboard and the way the satas are labled, I forget if the RAID needs to be connected to a certain sequence of them? Also I found a picture of enabling raid in the BIOS and I see I had 2 set for enabled, but they are labled differently than what is plugged in. How can I figure out what is really what channel and enable raid on it?
 

Everyone is scare to take a shot at my problem lol?

Sounds like the MBR has moved. If the ssd is what you want to boot from, you can try unplugging all other drives and boot with just the ssd. Use the windows disk to fix boot on that drive, if that is all it is should take a couple of mins at best.

If that works for the ssd and boot, then you can try to rebuild the array through the irst control panel. 

Ill give it a shot, the ssd boots when the hdd is plugged in but will not boot alone and gives the error message i posted above in picture 2. Ill let you know what happens.

nvm I got it, you check the health of your drives?

Speed fan indicates no issues for the health

Just as an update, (i was busy with school and then active duty so just dealt with it) the plugs dont seem to matter, the problem was one of the drives wasnt working properly so when I pressed "R" it didnt show up the 2nd drive to rebuild it. I just deleted 1 drive and was able to rebuild from it.
So the story is the location of the plugs didnt matter.