Sorry you are having trouble! The link i posted above tells you to go
here to set up your emuMMC. That site shows you how to setup multiple emuMMC's, which is preferred in your situation from what i understand. One partition for emuMMC stock and one partition for emuMMC CFW, you wont be booting into sysMMC anymore except to run caffeine when needed if at all. One partition is ok if you are never going to take it online, its up to you what to do here. Make a nand backup before you do anything else as this is what is needed to make your emuMMC and is required if making two partitions. You will want the entire SD card formatted to fat32. Everything is laid out for you
here like i posted previously but this time start from the very beginning.
The only thing i would add is have your SD card formatted to exFat when making your nand backup so that its one file and not a bunch of small ones. Or use a separate SD card for that process. This of course is just my personal preference when making a nand backup and not necessary.
The overall process should look like this.
1. Prepare SD card for partitions
2. Put latest required files on SD card (Atmosphere, pegascape, hekate, sigpatches)
3. Launch Caffeine
4. Make full nand backup plus boot0/1 from hekate
5. Place backup on PC and merge the backup files
6. Flash backup to partitions
7. Import the newly flashed partitions within hekate
8. Have fun!
I know that there is more involved but Im not going to go in complete detail as all that detail has already been given within the above guide i linked to.