I ran into this problem... I have a modchip, and I want to install DVDX so I can load ROMs from a DVD. No problem with that, except... The DVDX in the HackMii Installer does not support modchips, so if I want DVDx, I will have to use the old PatchMii installer. BUT WAIT! The PatchMii Installer uses IOS254, the same as BootMii. After searching around for a bit, I finally found a solution to my problem, and hoping it can help some others.
STEP 1 - Install What You Want
First thing to do is pull up the HackMii Installer, and install The HBC (If Needed) BootMii as Boot2 and BootMii as IOS. DO NOT install DVDX!
STEP 2 - IOS 253
xan105 at GBATemp created a modified version of PatchMii_Core. What this does is installs PatchMii as IOS253 instead of IOS254, which BootMii is using.
The .RAR file comes with the two things you will need... The IOS253 PatchMii_Core, and the original DVDX installer. This is as simple as dropping both of them into the apps folder on your SD card, and running the PatchMii_Core IOS253 installer.
STEP 3 - READY FOR DVDX
After the modified PatchMii_Core is finished installing, you want to load up the DVDX installer. Instead of selecting PatchMii Install, like we would have back in the good ol' days, choose Advanced Install. Once you have chosen Advanced Install, scroll over until you find IOS253, and then press Install.
There you have it! You can now have DVDX installed on your chipped Wii, without harming the BootMii IOS.
I take no credit for the software used in this tutorial.