I don´t understand the point 1 ... why do you need to separate the information in two tables?? Don´t they have the same dimensiones? You can use the option "Relative" in the options of the expressions sheet to get the percentages, else you need an expression using the same formula that table1 but adding sum(total Whatever) as denominator.
Question 2: I would do it on scripting if the rule is always for the last 2 months, if the rule depends on the selection of the user, it should be done in the chart
I'm attaching a sample qvw I've created to check your item 2 requirement using set analysis. You can set the number of months for the calculation.
About item 2, I agree with Jose. Especially in cases when your calculation is complex, it is preferable to leave the heavy calculation "in the background" during the reload, so that the user experience is good when refreshing the charts.