Edit: forgot to mention this is my first guide so bear with me here,
Ok guys, I said I'd try to get it working on an Epoch server and post my findings here for others to be able to do the same. took me a couple days of toying but i got it figured out. I'll break it down to make it as simple a process as I can, so even people new to editing can do it but either way its slightly time consuming.
1. First things first: the epoch mission file for arma 3 is currently encrypted in some way, shape, or form so we need to take care of that. You can undo/redo this encryption with a program called Eliteness by Mikero.
Eliteness link: https://dev.withsix.com/projects/mikero-pbodll/files
From that link go a head and download Eliteness, DeOgg, DePbo, DeRap, and Rapify and install all to your computer. (You may also want to look at the read me).
2. Download your current mission file from your server, (example: epoch.Altis.pbo), and put that somewhere safe on your computer. keep this one as a back up in case something goes wrong editing your mission.sqm and you have to revert. Now download another copy of your mission file (or copy the one you have) and use that to edit.
3. Make sure you have Ryans Zombies and Demons on your computer and your server (I use FTP, no dedicated box here :-/ ). Now go ahead and boot up arma 3 and go into the editor. Create a new mission, doesn't matter the name but make sure its for the map you are using (obviously). Now go ahead and place the zombies you want around the map, set what you want them do, how many there are, waypoints, ect. Once your done editing go ahead and "save as" your mission file under a random name, (really it doesn't matter what you name it but I used altiszeds as a name if you want to use that), to make the file easy to find when i go to "save as" i usually export it to MP missions, and it pops up in your mpmissions folder in your arma 3 directory.
4. Now its time to dencrypt your epoch mission.sqm. locate the epoch.altis.pbo you would like to edit. Use either Eliteness to depbo the file, or use PBOmanager and extract it to a new directory. (Id like to note I dont use eliteness to depbo, i prefer pbo manager for that.) Locate the mission.sqm file. Open up Eliteness. Locate the mission.sqm file on the left side navigation window. Open/view by right clicking it. ***NOTE*** it seems that when trying to derapify the epoch mission it doesnt always derap the whole file but only 1/2. You will need to derapify and view the file in eliteness rather than resave the file. copy all the text from your mission.sqm you're viewing in eliteness and paste it to a new notepad ++ file. save this file as mission.sqm, make sure its not just a txt file. and there you have it, you can now view/edit the epoch mission.sqm. though dont poke around too much you might break it :P
5. Next Depbo the new zombie mission you just created in the editor, altiszeds or whatever you named it, and open up that mission.sqm. look under the class groups you should see something like:
Copy everything from Items=9 to the bottom of the groups section.
6. Open up the new dencrypted epoch mission that you just made and locate the bottom of the groups section in this file, should be below the line that says item99 and just before class Markers. copy the items you got from your altiszeds file in the step above and past it into the class Groups below item99. now make sure your syntax is correct meaning your brackets still line up and no extra semi colons stuff like that otherwise it wont rapify and ultimately wont work. Go through the new items you just pasted and change the item numbers to correspond with their position in the class groups list. For example if you just pasted after item 99, you will need to change your first item to 100, second to 101 ect. ect. once youve changed all the item numbers go ahead an scroll up to the top of the class Groups section and locate the line items=99, change 99 to your new total number of items. last thing you need to do in there is locate addOns = section at the top and add "ryanzombiesfunctions" to the line of addons. save the file.
7. Open Eliteness back up and locate your newly edited epoch mission complete with zeds and right click it and open/view then rightclick again and rapify it, this should re-encrypt the epoch file. Note that Rapify will not work if there are errors in your mission.sqm, luckily it should tell you which line the error is on. now take this new mission file put it back into your extracted epoch.Altis.pbo folder and repack the PBO with PBO manager.
8. Re upload your new epoch.Altis.pbo to your server MPmissions folder. edit your server command lines to include ryans zombies boot server. your golden.
Hope this helps someone :)