I'm not sure exactly what guides you followed so I'm just gonna start from the beginning. Only because when you talked about converting and changing the name of the ISO files, it raised a red flag.
1 - Converting: I'm not sure how you're obtaining your ISO's (whether you're finding the files online or backing them up from your own discs) but either way you shouldn't have to convert them. The file should be fine the way it is, unless you wanted to shrink them to try and save disc space, but that's something else all together.
2 - Renaming: You DO need to rename them, but you don't need any special tool to do it. You just select the ISO file on your PC, right-click, and rename the file right from there. So say the file is "StarFox-Assault.iso" you'd rename it to "game.iso" Every single GC ISO file will be named "game.iso", and because of this you will have to place each "game.iso" file into it's own individual folder. From there you can name the game folder whatever you want. For naming the folders, I usually follow the format "Name [GAMEID6]". So lets say for Star Fox Assault, I'd name the folder "Star Fox Assault [GF7E01]". But honestly I don't think it matters how you name the folder. All you need to remember is that each ISO file will need it's very own folder.
3 - Location: Now that you have the ISO files renamed and placed in their own folders, you'll take all those folders and drop them into a folder that's just simply named "games". Then place the "games" folder in the root directory of your harddrive.
That should have you covered for file names and locations. And it seems that you've already formatted the harddrive correctly. So you should be set. As far as Dios Mios, I recommend installing the newest version (2.10). Yes it'll have some compatibility issues with certain ISO's, but it's easily the most complete version of DM.
If you're installing the DIOSMIOS 2.10 wad (not lite), and you're running everything from WiiFlow, then you don't need anything Dios Mios related on your SD card at all.