Scrubbing basics:
Wii isos have game data on them. This data is signed to make sure it is not changed, only Nintendo can sign it properly but they messed up the check in earlier firmware versions and we can make it so that is appears to be signed (well enough to fool the very broken check in earlier versions: http://hackmii.com/2008/04/keys-keys-keys/ and http://debugmo.de/?p=61 explain that one).
This game data need not take up the entire disc which is a set size.
Unlike DS roms where the extra space is at the end of the file the wii has it throughout the disc and as such all wii isos are the same size (once dual layer and single layer have been accounted for).
In most cases this extra space is essentially random data which can not be compressed via normal (zip/rar/7zip) methods.
This extra space is also not covered by the wii signing so you can change it as much as you want without issue.
The wii scrubber on the most basic mode replaces the random data with 00's (long chains of which are trivial to compress)
The iso is unchanged however in any way that matters to the game or the wii.
The wii scrubber will leave the iso unchanged in file size which is kind of useless on the face of it but now you can compress it in a zip/rar/7z or you can use a drive space compression program (windows/ntfs has one inbuilt), you can use a transparent compression method (many apps allow you to browse zip files as you would directories) or you can do something like put the big wii iso (as a whole file) into a compressed iso format and then put this new compressed iso into a fake drive like one daemon tools gives you (this will mean on the drive you computer and more importantly the flatmii software will "see" the full iso but in reality it will still be compressed).
"regardless of which IOS I am using"
I will have to ask you about this one, do you mean IOS as in the small operating systems used by most wii code to interact with the hardware or was that a typo and you meant to put ISO?
To answer that one Flatmii is a drive replacement (as far as the wii is concerned it is a normal drive working how it is supposed to), it uses your PC to do some of the hard work of emulating the wii drive and the chip to do the rest. As we do not know the communication protocols between the USB port and the flatmii we have to use the software from the flatmii team, this software will only load straight up wii and GC isos (which come with a .iso extension format) and as scrubbed discs are still perfectly valid as far as the wii is concerned.
A note, some scrubbed discs can remove updates and the like from the disc. This breaks the signing of the disc and we then have to "fakesign" it but as long as your wii will accept it (any wii below 3.2, you can hack 3.3 and 3.4 (all versions) to accept it and 4.0 is presently unhackable unless you updated via homebrew methods).
Wii isos have game data on them. This data is signed to make sure it is not changed, only Nintendo can sign it properly but they messed up the check in earlier firmware versions and we can make it so that is appears to be signed (well enough to fool the very broken check in earlier versions: http://hackmii.com/2008/04/keys-keys-keys/ and http://debugmo.de/?p=61 explain that one).
This game data need not take up the entire disc which is a set size.
Unlike DS roms where the extra space is at the end of the file the wii has it throughout the disc and as such all wii isos are the same size (once dual layer and single layer have been accounted for).
In most cases this extra space is essentially random data which can not be compressed via normal (zip/rar/7zip) methods.
This extra space is also not covered by the wii signing so you can change it as much as you want without issue.
The wii scrubber on the most basic mode replaces the random data with 00's (long chains of which are trivial to compress)
The iso is unchanged however in any way that matters to the game or the wii.
The wii scrubber will leave the iso unchanged in file size which is kind of useless on the face of it but now you can compress it in a zip/rar/7z or you can use a drive space compression program (windows/ntfs has one inbuilt), you can use a transparent compression method (many apps allow you to browse zip files as you would directories) or you can do something like put the big wii iso (as a whole file) into a compressed iso format and then put this new compressed iso into a fake drive like one daemon tools gives you (this will mean on the drive you computer and more importantly the flatmii software will "see" the full iso but in reality it will still be compressed).
"regardless of which IOS I am using"
I will have to ask you about this one, do you mean IOS as in the small operating systems used by most wii code to interact with the hardware or was that a typo and you meant to put ISO?
To answer that one Flatmii is a drive replacement (as far as the wii is concerned it is a normal drive working how it is supposed to), it uses your PC to do some of the hard work of emulating the wii drive and the chip to do the rest. As we do not know the communication protocols between the USB port and the flatmii we have to use the software from the flatmii team, this software will only load straight up wii and GC isos (which come with a .iso extension format) and as scrubbed discs are still perfectly valid as far as the wii is concerned.
A note, some scrubbed discs can remove updates and the like from the disc. This breaks the signing of the disc and we then have to "fakesign" it but as long as your wii will accept it (any wii below 3.2, you can hack 3.3 and 3.4 (all versions) to accept it and 4.0 is presently unhackable unless you updated via homebrew methods).
