Dop-IOS Mod and cIOS Patchmii Installer are completely different, neither can be considered better. Like almost everything else, both will run normally regardless of your system menu version. However, you need the trucha bug in IOS 36 to use cIOS Patchmii Installer. Also, you need to run it twice if you have the stub IOS installed along with system menu 4.2; otherwise it will remove the stub, but not install cIOS. cIOS Patchmii Installer can't brick your wii.
Many of the features of Dop-IOS Mod require a trucha bugged IOS, which it can patch for you. You shouldn't use Dop-IOS Mod (or anything else that modifies your wii) unless you know what you are doing. It has many useful features, but if used incorrectly, it will fully brick your wii.