I have had it set up like this since I put this PC together, actually never really had a problem, but I was just thinking if it would be better performance-wise to actually have the boot-drive on the first SATA connector.
When I open up disc management it shows my RAID storage drive as disc 0 and my main disc (with the OS on it) as disc 1. I suppose, normally it should be the other way around?
If I swapped the connectors on my motherboard, would that only be an issue of re-adjusting the BIOS accordingly or could this really mess up Windows?
No it won't affect performance, at least not in any human-perceptible way. Its not like the system will keep trying to find your hard drive on SATA1 after it already knows its at SATA2.
I'm now a little confused as to your setup. I thought you had a single drive with a software RAID1 mirroring two or more partitions. Do you have two discs? As for the disc 0 vs disc 1 your system may just read RAID 'devices' before normal devices, such as an older system would read floppy drives before IDE drives.
If you swapped the connectors you shouldn't have to change anything in BIOS. It would possibly mess up your MBR (master boot record) which would mean restoring the MBR via a Windows boot disc. It might just work though, eg if you had two devices connected at SATA2 and SATA3 and just shifted them both down one connector perhaps it would still read the first device first, whereas if you just switched the SATA3 drive to the SATA1 connector it would then change the order. This is based off of my Linux knowledge I am not positive how Windows reads disc order, it might just ignore where its connected and use UUIDs (universally unique ID) which is different for each drive and would then work no matter which connector you switch to.
It sounds like it works now, so I wouldn't mess with it unless you have a real reason.