I faced a similar problem - my best cards are are stored in 3x3 sheets, rares first, then mythics. Each section contains cards ordered by collector's number. I found it very inconvenient to type cards' names by hand.
To overcome that problem I had to write a small program that shows cards in the same order as they are stored in album. I choose the right edition from the list on the left, then a list of cards appears. As the list is filled with cards, I nvigate with up/down arrows and press SPACE and ENTER to denote the number or english and non-english cards I own. After I'm done with a certain edition, the tiny buttons (labelled '=> Eng' and '=> Oth') under the table copy the matching havelist to your clipboard.
With that text in clipboard I paste it into the textbox that appears when you choose "import cards".
If the application won't start, you'll have to edit with notepad the provided .config file - to point the program at the folder where Magic online is installed.
Drawbacks:
1. Requires up-to-date client for Magic Online v.3 - the what they call "current version" (my program extracts cards database from there) http://mtgoinstaller1.onlinegaming.wiza
Helper.exe
2. Requires Windows and .net framework 4.0+ - http://www.microsoft.com/en-us/download
x?id=17851
3. No warranties of any kind come with this software, use at your own risk.