Mark's right, you don't usually drain, just replace. Use fresh fluid to push the old stuff out, but if you're emptying the master cylinder don't refill it, just let it empty out.
Once the new one is replaced then just refill and pump out of each corner - as Mark says, start with the one furthest away and work closer to the master cylinder until it all looks bubble free and clean.
I'd avoid silicon fluid unless you're intending a rebuild of the entire system with new components.