After a bit of time working on it, I now got WAIO working perfectly on Supercard DSone and DSone i
Step 1: Install YSmenu. There are millions of walkthroughs for this, so go find one and use that.
Step 2: Download WAIO and copy the waio.nds to another location, like on your desktop. Copy the _rpg folder into the root of your card from there.
Step 3: Download the DLDI patcher:
here
Step 4: Copy the didl.dldi from the _dsone folder to the folder where you have DLDI patcher.
Step 5: Patch the waio.nds file
Step 6: Copy the waio.nds to the root of your card and rename it to ttmenu.dat. Now I mean copy the patched file, don't move it since it will be need later.
Step 7: Rename SCFW.SC to EOS.NDS (or anything with .NDS at the end) It can now be launched as a homebrew and work only using a Supercard DSone(i). If you try to launch it through another card it will not work.
Step 8: Download this file:
here. All you need is the MSFORSC.NDS file from it. So just copy the MSFORSC.NDS file to the root of your card.
Step 9: Download and install MoonShell2Tools incl. Link Launcher:
here. Go into the extlink folder in the moonshell2 folder and edit the inilink.ini making sure it is also in the proper location for the Ysmenu and Ysmenu.ini. (example: YSMenu=/YSMenu.nds
YSini=/ttmenu/ysmenu.ini)
Step 11: Now with the copy of the patched waio.nds copy that one into the root of your card and rename it to _DS_MENU.DAT
So you should have both TTMENU.DAT and _DS_MENU.DAT, both should just renamed version of the patched waio.nds.
Finally just safely remove you card and there you go, WAIO is now the primary firmware of your card and it should load roms through YSMenu.
The _DS_MENU.DAT file allows you to change your themes without it having an error.
Also the soft-rest isn't the same as WoodRPG (R+L+A+B+?). It uses the YSMenu soft-reset which is R+L+A+B+X+Y
EDIT: I should have added this along time ago, but I would like to credit Xenon++ for being a big help in making this walkthrough. If he didn't help me so much I would have never known to have dldi patched the waio.nds file and still would have been at stage one. So thanks Xenon++!