If you're desperate for heat, you can switch the receiver next to the boiler to ON. That's the switch in the middle next to the light.
To pair up the transmitter after your replace the batteries:
1. turn the receive back to AUTO which is the middle setting
2. on the transmitter, press OK twice to access the menus
3. find the Pair menu using the scroll ring and then press OK
4. press OK again and you should see the pairing icon which I think is supposed to be a tiny transmitter mast
5. you now have 10 seconds to press the sync button on the receiver before it self-destructs - the sync button is the one on the right
No, seriously, you have 10 minutes to get the pairing so don't panic. And it won't self-destruct but you'll have to start all over again. Once you've pressed sync, icons will flash on the display and the LED will flash on the receiver. Hold your breath and it may all work. If it fails then the LED will flash really fast, or it may just all give up after 10 minutes. Once you think it worked, manually set the controls so the heating should come on and see if LED on the receive comes on and stays on. Obviously the boiler should also fire up.
Manual mode switching back to auto even if you only just set it is stupid, but it seems to be standard on this type of controller. omega already explained good ways to deal with this. You can have the automatic controls set to a relatively low temperature 24 hours a day and control it manually, or have it in holiday mode which is a really low temperature all the time and control it manually. Or just a small number of time slots, like maybe "day and "night", so you can keep track of where you are.