I've been searching about this a lot however couldn't manage to get the answer.
When I use Canon's auto mode, it triggers pop up flash to focus on a subject and then take a shot in low light.
However using manual mode with autofocus(single focus point) doesn't triggers the pop up flash to focus even if the built-in flash is already popped out.
Is there a setting or something I could use to trigger pop up flash to focus when in low light
Yes, there is a setting. You can use your pop-up flash as a focus aid while in manual exposure if you enable it in your Custom Function menu.
There are also some other options which may not be quite as distracting to use .....
Most external flash units emit a red colored cross hatch pattern which makes it easier for the individual AF points to lock on to and to allow the camera to Auto Focus in low light conditions.
You can use the AF aid with the flash turned off on most cameras, and there is also at least one low cost accessory available to do this.
Yongnuo Announces New AF Assist Accessory For Canon Cameras
Another option might be to find a way to attach a light to your hotshoe that you can turn on and off as needed. (like a video light or flash light)
