Addition of MgCl2 is not a problem just reduce the volume of water that you used for the master mix with the same volume of MgCl2 solution that you add to the master mix.
Reduction would be a somewhat problematic if you are using a kit, if not just make/buy the buffer without MgCl2 and add less MgCl2 to the master mix.
Regular PCR buffer normally added 1.5mM of MgCl2. If you want let's say final concentration of 2.5mM MgCl2 in PCR, you should add 1mM of MgCl2 into each PCR reaction. The volume of MgCl2 you need to add can be calculated using the equation C1V1 = C2V2, which will be depending on the stock concentration of your MgCl2 and the total volume of your PCR mix.
As Raditijo mentioned, it will be a lot more troublesome to reduce the MgCl2 concentration in the buffer. The easiest way to do is buy MgCl2 free buffer and add MgCl2 separately into the mix.
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