Let me share my experience with you, as I just purchased my 2016 OW ST3 on Saturday. TL;DR version is at the very bottom that will cut to my recommendations for you. If you're interested in the narrative, continue reading
I live in an area where Focus STs are definitely not plentiful. There were very few dealerships within 100 miles of me that had any Focus STs on their lot, and there were virtually none that had what I wanted (Oxford White, ST3, moon roof, machined wheels). I did a lot of searching using various third party sites (Edmunds, Cars.com, TrueCar, CarsDirect, you name it) to look for something resembling what I wanted.
I started with TrueCar, which sent out inquiries to two TruCar certified dealers. I received an automated response from one of the dealers indicating they got my inquiry, but they never ended up even reaching out to me. The other dealer contacted me via email to tell me they had a white Focus SE on their lot... obviously not what I was looking for. I emailed back and forth with them telling them exactly what I wanted, and they did an inventory search and were able to locate exactly what I wanted (but did not mention where). Discussed back and forth, but the dealer was not really interested in cutting a deal with me, so he wished me "good luck."
When contacting the next dealer (directly, I might add), I had the exact car I was looking for (VIN and all), so I asked them if they could locate it for me and strike a deal... I made sure to mention that I was interested in making a quick purchase and was a serious buyer. Unfortunately, the internet sales guy I spoke with had to be the least competent individual ever. I gave him the VIN and he asked me if I had the stock number so he could locate it (who works for Ford, here???). Long story short, he emailed and called me a few times to check and see if I was still interested (even though I was waiting on him to locate the car). Eventually, he calls me to tell me he has a car and would like me to come in for a test drive. I ask him if it's the one I wanted, and I come to find out it's a black ST3 with snowflakes. Needless to say, he didn't listen to a word I said and I ceased any further deal-making with him.
Next dealership - I contact them through their website and tell them I'm shopping around for a specific vehicle and looking to make a purchase very soon if they can give me a good deal. I provide color and options, but no VIN. Sales manager contacts me a couple days later with a VIN scan... just so happens to be the same car I was looking for. He asks me to come in and talk numbers, so I make the trip (about 1hr) one weekend and we chat. He plays a little hard ball, I walk out. We e-mail back and forth and over the next 1-2 days he gives me a little better offer. I told him both at the dealership and via e-mail what I was looking for price-wise. We negotiated a little more back and forth, and we agree upon a price. He sends me an electronic offer to sign.... but when I review the details, I notice there aren't any. No VIN, no car information, etc. I email him back to ask if the offer I'd be signing would be for the car with the VIN he sent me originally. He calls me back (instead of responding in writing) to clarify some things. I ask him again about the car specifics and tell him I'm not signing anything until I know what I'm signing. He tells me that he's using the information he sent me "as a guide" and is trying to locate a car that meets my needs. I tell him to come back to me once he has a car and I'll come in to sign papers. A few days later, he contacts me to tell me he found a black ST3. I reminded him that I was very specific with what I wanted. He tells me he was unable to find an ST available for trade that matches my description. I'm pretty annoyed at this point, since it seems like these dealers aren't actually understanding me when I tell them exactly what I'm looking for. At this point, I move on again.
I expand my search criteria and finally find the exact OW ST3, down to the VIN #, at a dealership just about 230 miles away from me (just outside my previous search radius). Even better, the deal listed on their site is significantly cheaper than the price I had previously agreed upon with the last dealer for what I thought would have been the same car. I go to the dealer web site and submit a request for price quote. I get an email response by the next day. Literally 1-2 days of emails and phone calls and we strike a deal for $26k OTD before TTL (I have to pay that in my home state since the dealer is out of state) without me ever setting foot in the dealership until I come to sign the papers. Turns out to be the quickest and easiest deal I've made and I drive the car home happy.
TL;DR - Contact dealerships directly instead of through third party sites. If you know what you're looking for, be specific. Also make sure to let them know you're serious (sometimes I get the sense that they don't think you are unless you say so). You'll likely find a better deal if you find a car on the lot than if you work with a dealership to locate.
Good luck!