I create click tracks for myself where the metronome will drop out for a bar. In other words, the metronome will click for one bar and go silent for the next bar and then continue to alternate like that. When I practice along with this I try to make sure I'm right there on the one when the click comes back in. You can create practice tracks like that for yourself using almost any recording software.
Another tip is to practice with a metronome and play around the click. In other words, I will set the metronome to a very slow bpm (like 40) and then treat the click as one beat in a 4/4 bar. First I will treat it as the one, then the two, then the three, and then the four. Then I might treat is as the 'and' of a beat. This works really well if you play a really good syncopated groove but start out just playing straight quarter or eighth notes.
Just in case you don't quite get what I mean I'll give an example. Lets say you are going to "treat the click like it's three." Set the metronome to 40 bpm and every time you hear the click pretend that's where the third beat of the bar falls. This means that the actual tempo your working with is 160 bpm but your click is only reminding you of the tempo once in a bar.
I hope that makes sense and you find it helpful.