Hi,
The solution to your problem is very simple... (with the 1st game anyway). If you already know how to self-boot games, then you are almost there. : )
Ok, 1st - rip your files with isobuster, or however you made the game self-bootable before.
2nd - Get an "IP.BIN" (you can use any IP.BIN from any game, or you can make your own).
3rd - Edit your IP.BIN with IPBIN4WIN. You can get it here:
http://internetconvoy.com/Downloads/IPBIN4WIN.zip
Just start IPBIN4WIN, put a check in the box of all the options you want, and press "patch." This download also includes IP.BIN's for several games. You can use any one of them though... just make sure you put a check in the box for "VGA Support" and change the name of the game to whatever you want.
4th - That's it! just put that new IP.BIN into your folder when you make an *.iso to use with "bin2boot" or insert it into your *.iso with "ipins.exe" if you're using the "echelon" method.
Now, for "Skies of Arcadia"...... That one's not so easy for me. I have the same question. I haven't succeeded at making a working backup of it yet. It will boot to the "echelon" intro where you can put in your cheats, but then it will reset when you go to start the game. It seems "echelon" made the 1st_read.bin different than in the other games. It uses a special method of unzipping things on-the-fly in order to fit the game onto 2 CD's. "Binhack.exe" just gives an error message if you try to mess with it. I've tried making an *.iso and using bin2boot, but I haven't gotten a working copy yet, (error stated above).
If anyone knows how to do this one, I would love to know also. I've been trying at it....
Hope I've helped you.
Later,
-Ex