I haven't been over for a few years but the last few times I've been it was from the Queen St bus station (the one near Jalan Besar). You buy a ticket for the express bus and get that - the SBS one (170 I think) stops all the way along Bukit Timah Rd apparently so don't get that one.
when I went, the ticket from Singapore was one way which they didn't tell us - we assumed it was return - not so, had to buy another one for the way back so check that before you come back (there was a ticket booth the other end before immigration).
It's a bit of a funny system too (or it used to be). You have to get off the bus at the checkpoint, go through the immigration and go down and get on another bus to go across the causeway (this could be your original bus or a different one from what I remember - they just all queue up and leave when full - so keep your ticket in case you have to show it again). Then you go through Malaysian immigration the other side.
Have fun
