Basically, simply stick the chemicals into the system, wait for them to do their work and then flush them out.
From the instructions provided by a manufacturer of the type of cleaning chemicals used:
"Ideally the system should be powerflushed to remove any existing treatment and contaminant. Fernox Cleaner F3 or Cleaner F5 should be added to system water and circulated hot for at least one hour. After which the system must be drained and flushed until the water runs clear. The cleaning time can be extended to up to one week for hardened iron oxides and limescale"
Source:
http://www.fernox.com/problem+solving/how+to+sheets/cleaning+a+central+heating+system