RYD,
When most people speak of rebalancing, they have a portfolio which has strayed from their desired asset allocation, and need to bring it back in line; usually on an annual basis. In these situations, a person would simply sell some assets from an asset class which have increased in value to purchase more assets in an asset class which have decreased in value. Classic sell high - buy low strategy.
In reading your post, I still have the following questions. Are you looking for help in establishing an asset allocaation? Or have you already decided on a target asset allocation for your portfolio and now wish to move your porfolio to this allocation?
If you are trying to establish an asset allocation, then you are going to find as many opinions and methods as there are people. You probably don't need software to solve this problem. There is a software product for professionals called "Allocation Master" which attempts to build an assets allocation along the efficient frontier. I think it costs something like $500 and is intended for financial planners and the like.
If you are trying to move an existing portfolio from a position of no asset allocation strategy, to a new desired long term strategy, then the question is more along the lines of "How quickly should I make a drastic change in strategy?" If the changes are significant, then I would suggest moving assets slowly over a period of 12-18 months using some form of dollar cost averaging, if this is practical.
Have I in any way more closely identified the intent of your question in my comments? Let us know.
Red