Well, Here is the method for you to make your DSTwo support 3DS new firmware V2.0.0-2.
IF your 3DS is still in old firmward,means you didn't update it to V2.0.0-2, just feel free to update the patch and install it in your nintendo 3DS.
I confirm you can update the DSSTWO using your N3DS.
Mine was on version 1.1 (EU version)
1) I copied the dstwoupdate.dat to the root of my memorycard
2) started the DSTWO, which asked if I wanted to update (ofcourse I did!)
3) update succesful
4) removed the dstwo (just to be cautious) and updated the 3DS firmware (v2.0.0-2E)
5) After reboot, insert dstwo and... tadaaa... all works!
If you have already updated your 3DS to 2.0.0-2 , well ,Noticeon't update in your 3DS, you need to take a DS/DSi to do the update.
1.Put the file from the archive in root folder of sd card.
2.Insert flash card in ds and start.
3.It'll ask you to update.