Unfortunately not. When you enter your income into EEBA you can choose how much you want to allocate to each Envelope, but not by percentage. In most cases, it may be more useful to think of your budget in terms of actual numbers. When I look at my budget, I know that I spend about $100 a month eating out. If I make more in one particular month, I'd like the extra to go to something else, not assume that I will spend more on eating out.
Of course, we all budget in our own way, and I can see how a percentage based fill could be easy to use and convenient. I've added it to our requested features tracker, thanks!
I'm adding my voice as well. In fact, this for me has been the number one reason why my interest in the app has waned, because I have to do the calculations myself anyway. So for now I've resorted to a spreadsheet where I can decide if I want a particular category to be a % or a fixed number. But I'll be happy when this feature comes out and will probably be right back.