I just fiddled with it a bit and got some accurate numbers. I haven't tried with the download that you have to do to get the Quebec taxes, but I got accurate numbers (to a few pennies) based on my Ontario pay.
It takes a few steps, but here's some hints.
Use a mid month pay statement for comparison. We are technically paid montly, and they give us an advance on the 15th. The calculations are all based on 12 pays per year, which is shown on a mid month pay.
Use an early year pay. Most of us max out on our CPP/EI contributions at some point in the year. Using the CRA calculator, you can account for the fact that you may have maxed out on those contributions, but it gets more complicated. Use a pay from early in the year for the comparison to make it easier.
Enter your gross montly pay then run the calculation and that should give you the right numbers for EI and CPP. Ignore the tax numbers at this point - they're wrong.
Now go back and look at your pay statement. Subtract your superannuation amount from your gross pay. Go back on the CRA calculator and enter that number as your gross pay. Reason - we don't pay tax on our pension contributions. Also, if PLD is applicable, enter it now in the "non cash, non insurable" box (PLD is taxable). Run the calculator and that should give you a pretty accurate number for the taxes that will be paid.
Now you have your EI, CPP and taxes. Comparing those numbers to your current pay statement should give you a pretty good estimate. At least it did for mine with what I did above.
Good luck!