A lighting circuit needs to supply Live to the Lamp via a Switch to be able to turn it on and off.
Permanent Live is routed to the switch and the returning wire, known as Switched Live, connects to the lamp to give On/Off control.
You appear to have bypassed the switch and therefore will have no On/Off control.
Your best approach may be to call in a specialist. If you remove the ceiling roses to fit your flush lights you will lose the advantage of the four connector blocks in each rose - Live - Neutral - Switched Live - Earth. An electrician will be able to tuck junction boxes up in the ceiling void for you.
Good luck...
Peccavi, November 2009