Hi Thnikkaman,
I'm just reading your post now, on 12/22.
I had this same problem several years ago, when I was playing Havannah. I didn't have a good way of analyzing my games... and it bothered me! So I ended up spending several weeks, as I recall, writing a little program to help me. I named the program "Havannah Helper."
http://www.edcollins.com/havannah-helper/index.html
HH was VERY useful for me, during the entire time I was playing Havannah. It made my games more enjoyable, and surely helped me to a few more wins than what I would have had otherwise.
Now, I definitely don't have the desire or time to write a similar Dots and Boxes program for you, (I'm not a D&B player) but I did have a couple of extra hours this evening, so I put something together that MIGHT help a LITTLE bit.
It is NOT the all-purpose program you're expecting, trust me. Sorry. But maybe it's a little bit better than the method you're using now. If not... well, that's okay.. it was good practice for me to write it.
This program is an Excel program, and uses Visual Basic macros. Thus, it requires Microsoft Excel to run, which you might not even have for all I know. If you don't... sorry. But it was quick and easy to create.
You (or anyone else) can download a copy of the program here:
http://www.edcollins.com/dots-boxes-assistant.xlsm
A small HELP tab is included. Basically, you just enter your Little Golem Dots and Boxes Game number in the appropriate box, and then click the DOWNLOAD button. The Excel program will then visit the Golem site and download your game and display it on the screen. You can then click on the "walls" of your dots and boxes game and try different lines of play. The program will automatically detect when a box needs to be filled in, and will do so, based upon whose move it is.
Prior to analyzing a few lines, click the SAVE POSITION TO MEMORY button. Then, when you're finished trying a line of play, simply click the LOAD POSITION FROM MEMORY button to retrieve the last saved position. From there you can begin analyzing another line.
Basically, that's about it.
It's not perfect, but it seems to work pretty well for me. I've been testing it for the past half an hour, and I can find no more bugs (but I know some surely still exist) so it's probably ready for you (or others) to use.
P.S. I'm REALLY SURPRISED there isn't already a Dots and Boxes program out there that does what you describe. No one's taken the time to write one yet? What's up with that? I recall seeing an Amazon program years ago that does this, and of course I'm also familiar with the Twixt program that allows one to analyze their games. (And, of course, there are dozens of different chess GUIs for us chess players.)
If I can put this little thing together in an single evening, surely a Dots and Boxes fan can spend a few weeks and put together a much nicer program.