Need an efficiant set-up for Dual Boot MacBook Pro with MLion and Yosemite for music production

I've used dual boot set-ups for 10 or more years now starting with a G5 with 10.4.11 and 10.5 using the original OS for multitrack studio recordings with Firewire MOTU 828 converters a Lacie FW drive and the original Strienberg 2x2 Midisport USB MIDI. I have a simiar setup with my macbook pro that was working great until recently when I decided to try and use Mountain lion exclusively and erase Yosemite for the extra space...

That was a mistake as the laptop became unstable and there was no way of simply eliminating Yosemite forcing me to reinstall it on a second smaller partition and that made things even worse.

here is some background on whats going on,

Everything was working great at first until I accidentally upgraded to 10.9 that broke the Midi drivers and the software so I created a second smaller partition and reinstalled 10.8.5 leaving the files on the original partition because of space and links and was able to carry on like before but it was unorganized when is came to managing the files and doing back-ups. I kept working like that until I had some time between projects and decided to back everything up and organize the files better by making 10.8.5 the main partition and figure out a better way to manage the large collection of sessions and sample libraries that accumulate over the years.

After finishing a large project I decided to back everything up reorganize the files and prepare to reformat the startup disk and make more space for 10.8.5. I also want to use my G5 that still running tiger into the mix because is has these amazing PCI M-audio converters that can take a hot signal from a mixer making it an ideal 4 track recorder for mastering mixes and as a file server for samples and audio tracks.. There where many glitches and issues trying to network the two machines and use the G5 as a broadcast server until I purchased a new Asus modem. It took some fiddling around but eventually everything worked although it may be the troubles where because of a bug that became a monster as I moved on...

The final part of this job was getting more space and have 10.8.5 as the primary and 10.10.3 as the smaller secondary and place the libraries and session files in the 10.8.5 partition as they should be making everything accessible and easier to manage...When I started recording to HD It was common practice to record on to a second drive to get a higher track count before resorting to higher buffer rates and making it difficult to overdub or track when the session gets near the end.. That less a problem these days as the Macbook's internal drive can handle a high track count, low latency while maintaining a huge processing load that's needed for plug-ins, samplers.. adding an audio server that also sync's to the virtual instruments can make it easier for bands to consider relying more on them as the devices are better handling one job the one device handling them all as it is when your in the studio.

Now the the issue... I tried 3 times to reinstall the system and that caused all kinds of problems that hopefully go away once the right set-up is figured out... I've clawed out of EFI and start up issues along with the help of apple care and finally have a solid working Yosemite partition at 200 GB and a clean 550 GB one waiting for a fully working backup clone that is on a firewire boot disk. The other attempts ended with kernel panics and crashes.. Those problems have been located and solved but come back meaning there is something else affecting the disks.. It's looks like there is only one way to set this up and that with Yosemite on the first partition and fusion drive..

Question is; What is the best way to avoid conflicts when locating the libraries, session files along with being the administer of 3 OS's Two computers and one Domain.... What use to work no longer does.. So I'm going to try again and update this post after cloning the second partition with the firewire one that is working..