Considering that this is potentially the most politically sensitive border, there is nothing to worry about with this crossing. Note however that the UN control/have a presence on the East Timor side. While the UN are around, Indonesia would find it difficult to do anything stupid.
If/when the UN depart, then this page can be ignored.
Park up and have your Immigration documents checked at the first offices you come to at the border on the left side of the road.
When I went to the offices, at first, I did not present my Police Travel Letter, obtained in Jakarta. There was a general air of uncertainty. When I presented the Police document, this seemed to satisfy everybody. Even though it did not say that I was crossing from Indonesia to East Timor on the paperwork.
Customs are further down the road, on the RHS.
I was able to change my remaining Indoneisan Rupiah (which is not a convertible currency outside Indonesia) with the customs officers.
Staffed jointly by local East Timorians and Australian UN/army personnel.
The local guys seem to do the inspections and the paperwork at the moment, while the UN guys are there as security in the watch towers.
The locals here exhibit the same attitude as any locals you'll meet in Dili who work alongside UN personnel. For some reason, they seem to hate every minute of their day. They do not have the same attitude as the locals in the villages through which you'll drive. The ones which wave at you with a beaming smile.
Pull up in the compound on the right. The customs here inspect your vehicle, and then take you to the office for stamping the carnet. They were only partly aware of what they had to do, so, depending on who is on duty, some instruction from yourself may be necessary.
Visas (for British citizens at least) are available on entry. There is a visa charge of US$25. Visa extensions are available, for US$30 per month.