Here are the two methods to put saves
Using PCSX2 and PS2 Save Builder
1.Download your save from
here
2.Open it with PS2 Save Builder copy the Root/ID select all files right click on them and choose extract,create new folder with the Root/ID name and extract the files there.
3.Open your ISO creator(I use Ultra ISO) drag-drop the folder with the files that you create and save as ISO
4.Make sure that your memory card's are formated or not damaged(run the bios and format the memory card if it's needed)
5.Open PCSX2 choose for video plugin ZeroGS,choose for CDVD Linuzappz ISO and configure Linuzappz ISO to load the ISO that you create(if you don't choose the ISO or the correct plugin PCSX2 will freeze when you try to enter in CDFS) .
6.File=>Open ELF and open Boot.elf
7.Choose Select: Config and press O,press O again on Default: go to MISC/ press O choose FileBrowser and press O again to return to Button Settings,then go to Ok and press O.
8.Now Choose Default: FileBrowser and press O,go to CDFS:/ and press O select the save and press R1 and choose Copy,return to .. and press O go to mc0:/ press O press R1 and choose Paste,wait the save to be copied and you are done.
Using Mymc
This program is extremly easy to use
Importing:
Open cmd(Start=>run=>cmd) drag-drop the mymc.exe add space(press spacebar ones) drag-drop your memory card add space write import add space and drag-drop your save that you whant to put into your memory card,and that's it

Here is an example:
"C:\Program Files\Mymc\mymc.exe" "D:\Games\Playstation 2\memcards\Mcd001.ps2" import D:\kingdom_hearts.max
Exporting:
Before exporting something you must know the name of the save
Open cmd(Start=>run=>cmd) drag-drop the mymc.exe add space(press spacebar ones) drag-drop your memory card add space write dir.
There you will see something like this:
BASLUS-20678USAGAS00 UNLIMITED SAGA
154KB Not Protected SYSTEMDATA
BADATA-SYSTEM Your System
5KB Not Protected Configuration
BASLUS-20488-0000D SOTET<13>060:08
173KB Not Protected Arias
You must remember the name in left(starting with B).
Here is an example:
"C:\Program Files\Mymc\mymc.exe" "D:\Games\Playstation 2\memcards\Mcd001.ps2" dir
After you know the name it's time to extarct.
Open cmd(Start=>run=>cmd) drag-drop the mymc.exe add space(press spacebar ones) drag-drop your memory card add space write export and add the name of the save
It will export the save into(I don't know why there,maybe I'm not doing something right) C:\Documents and Settings\Your account name like PSU format.
Here is an example:
"C:\Program Files\Mymc\mymc.exe" "D:\Games\Playstation 2\memcards\Mcd001.ps2" export BASLUS-20488-0000D
If you want the save to be exported as MAX(Action Replay MAX) you must add -m after export
Here is an example:
"C:\Program Files\Mymc\mymc.exe" "D:\Games\Playstation 2\memcards\Mcd001.ps2" export -m BASLUS-20488-0000D
In the attachments I put all the files needed,just download three archives and extract one of them(it's spitted archive)
The archive also contains a movie on how to put saves into PCSX2 memory card using the original method
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P4 2.8GHz,6600GT,1024 RAM