You do not say the make / model of the timer or boiler.
Some boilers have a built in timer and some have an external timer.
My external timer has a flap covering slider switches that can select for both Hot water & Central Heating separately and independently of one another...each...
Permanently Off
Permanently On
Come on once each day for the set times
Come on twice each day for the set times
It also has the ability to select different on/off times for weekdays and weekends.
They often have a small battery to maintain the time of day clock during a power cut.
The boiler also needs mains electricity and fuel if it is to work.
Might be best to put your question in again with details of your setup...
Good luck...
Peccavi, October 2009