I don't work out a savings percentage, but I do include superannuation in my savings target. What with employer match and salary sacrifice reducing tax, I find that mentally a lot easier.
Depending on your age of expected FI, you should be counting super as part of your 25x. In my case, when I hit FI, I will be running down my non-super savings, while my super is going up. The total will remain the same.
As for splitting, super is taxed at 15%, while your first $20,000 or so of income is tax free. If you're not working it might be tax optimal to have ca $500,000 in the real world and the rest in super. If you're working, you'll need to work out the least amount of tax you'll pay across your years of working and not working.
My investment earnings do not count as savings in my calculations. That would be cheating!
You're right that super calculators are no use, as they don't let you tweak the most important variables. I just use Excel myself. I increment my savings by 4% a year, add on my planned savings in each year and go from there. This gives results in 2013 dollars. Use 6.5% per annum if you want it in tomorrow's dollars.
As an aside, are you aware that, by default, your super account is likely removing money for Death and TPD insurance, and possibly even income protection insurance? I'm surprised how many people at my work don't know that! The premiums for each increase each year, and you should make a decision to keep them, reduce the cover, or get rid of them entirely and review annually.