All the prior mentioned make great suggestions. I'll just provide my input as to what I dealt with. Initially, I was horrified of the click, loop, etc. But I just dug in and now I try to program everything to loop.
Anyway, I build my loops around the time signature. For example, if it's 4/4, I program a sound sample that cuts through with a snap, clap, cowbell, etc (whatever compliments the song) that is 4 beats so I constantly hear the four. Then I build other aspects of the loop around it (maybe a tamborine on 2 & 4, etc).
Now when you get good (someone told me this a long time ago and it's true) and "lock in" with the click or loop, you barely hear it or don't hear it all. That's when your time is right on. Sometimes when I play and this happens, it's scary, cuz I'll turn around and check my beloved Roland MC-909 to make sure it's still working.
But all is well, I've just "locked in" with the click.
To get comfortable with it, just do everything to a click or loop until you are comfortable. The same thing we do when we learn a new lick or beat.