I'm in Siem Reap right now. Went out to Koh Ker and Beng Melea with Ponheary Ly, also visited Koh Ker school (I'm behind hiyo by about a week). The road to Beng Melea is completely paved and in good shape. There is a "toll" per car but it's only a couple of bucks, and any guide/driver service should include that in the fee. There is an admission charge to Beng Melea of $5 and Koh Ker area of $10. Beng Melea is absolutely worth it. I was there a couple of days ago in the late afternoon and only about 5 of us tourists there. Very spooky now as it's rainy season and pouring off and on. The trip is combinable on a long day trip with other outlying temples such as Banteay Srei and Kbal Spean.
Koh Ker, I have my reservations about. If you are expecting spectacular temples, you will be disappointed. Frankly, I don't think the expense and distance are worth it for non-temple freaks, unless you are going long distance and can visit as an off-shoot. Or, like hiyo and myself, had other non-sightseeing activities in the area. The road to Koh Ker (once you leave Siem Reap province and enter into Preah Vihaar province) is VERY bad now and deteriorating by the day, as we are getting lots of rain now. Seriously reconsider doing this trip in rainy season. If you do so, you need to be in a high-clearance vehicle and even then, expect to get stuck. Or if you are able, ride a motorcycle. (Note to hiyo: my trip--a week after yours--was much worse. On the little side road to the school, we got stuck multiple times and even had to get the local demining camp truck to pull us out! The main road, only driver's skill kept us from getting bogged down several times. Other trucks on the road not so lucky.)
The rest of normal Angkor temples are wonderful, even in the rain. I much prefer this time of year (cooler, greener, more atmospheric), than the winter. And not too many tourists.