Do you want super luxury or just plain, fairly comfortable and not packed out air con? The cheaper air con buses can be just fine. Some people like the better facilities in the super luxury buses, though.

Regarding navigating the KL Puduraya bus station, you can simplify things considerably by ignoring the smaller operators and booking with Transnasional, who have a major presence in the station. It's not that big a deal, especially if you're at all used to Asia.

For long haul within Malaysia, the usual advice is to get to the JB Larkin station, which has a better selection of buses. To get to Melaka, though, you might as well just leave from the Lavender Street station in S'pore.