Mixing brake fluids is ok, PROVIDED your not mixing with silicone fluid. And the easiest way to change the fluid, i think, is to suck out whats in the resevoir, fill it up with new, and then open the bleeders at each wheel and just keep the resevoir topped up. If the old fluid is a different colour, you can stop when you see clean fluid, or when you think its had enough. To avoid making a mess, clear small pipe, such as used in windscreen washers work well when slid over the bleeder.
As for the alignment, could you elaborate? When you say alignment, what do you mean? Did you go from drums to disc, or just new discs?
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