Sometimes, a good travel agent can save you a bunch of money. If you have a relatively straightforward trip, Point A to Point B and back, book it yourself. If you are doing some side trips, etc, then a good travel agent that really knows Africa can help. For most hunts, I agree that booking it yourself is the way to go. If you want to add a trip to Vic Falls or Cape Town and tour the wine country, would go with a travel agent.
I've live in Nigeria for about 4 years and work with a lot of expats from all over the world. While living and working in Africa, most folks take advantage of travelling all over the continent and seeing the sights. So there's a pretty good network here of where to go and what time of year (avoid the rainy season), etc and what travel agent to use.
Two travel agents that I've used here are:
Go2Africa.com:
http://www.go2africa.com/?gclid=COnS0O3J78sCFaoy0wodZRcLLA
andBeyond:
http://www.andbeyond.com/about-us.htm
In 2014, I booked a "once in a lifetime" trip for my family and used Go2Africa. I was originally planning this trip for August and got a price quote. It was a lot of money and I told the travel agent I was going to have to think about it, maybe reduce it a day here or there. The travel agent asked me if there was something special about the timing being in August. I told her I wanted it during the cool months and a good water level at Vic Falls (not too much or too little). The travel agent told me "high season" started on July 1, so if I took the trip in late June I could save 25-30%. We went in late June.
I flew my 4 adult kids from the US, plus my sister-in-law and neice joined us, also from the US. Everyone met in Joburg and overnighted at the travel agent recommended African Rock Hotel (incredible place, food and service). We continued on to Zambia for a few days at Vic Falls. Did the dinner train trip and elephant rides while in Livingstone. Then traveled to Chobe Botswana for 3 days of photo safari, then back to Joburg. Everyone flew back to the US and we flew back to Lagos. All the arrangements were perfect, except one and that was a delayed Delta flight in the US. All our hotel arrangements, ground transportation, river crossings, clearing customs and immigration, side trips, everything were perfect.