Hi,
I've had experienced with SMT since the early seventies at MIT Lincoln Laboratory working with flat-pack 54 series TTL. I have to say, over the last ten years, everything, just about, I do in SMT. 10 years ago I tried etching my own; at the time I used TraxMaker for the PCB design, usually my prototypes were 2 layer and any hole plated-through. I found out, through the years that consistancy and repairability were always an issue. I also just plain never had the time to do the work. Now, remember, I'm talking professional R&D design and prototyping. I'm sure if I were doing it as a hobby I might not had gone the route I took that I am about to explain.
First, I generate the board layout from my design. I use OrCad schematic capture, so I generate a netlist for the connectivity and import that file into Protel's TraxMaker, now part of the CircuitaMaker Suite. I do the layout, check the output netlist against the input and when ok, I generate Gerber Files. I send the Gerber files to Advance Circuits; www.freedfm.com. The people do a design check for the hole clearances and traces etc for free. (DFM = Design For Manufacturing).They send me a quote and pdf files of all my layers. For prototyping, I generally buy quantity 3 for $33 each. With Shipping, that is usually about $119 US total. I then either hand solder the boards or order the parts through DigiKey.com or Mouser.com and have them drop-shipped to Advanced Assembly http://www.pcb-assembly.biz. They assemble my boards at a very reasonable cost and ship any parts overage back to me. I can literally finish a circuit design on a Monday and have assembled boards in my hands the following week on Wednesday..now that's quick turnaround!
Also, if you want to do the oven thing, get on to the www.freedfm.com website and order a stencil. You can then spread solder paste on the board, pop them in the oven and voila! Advanced Circuits (FreeDFM.com) has many good hints and good people to help you.