I have two MX 5000's and need to have them programmed. My question is, does it make a difference who you have program them? Is one person going to be able to really customize it and help me get the most out of all their features vs. someone who is just familiar with programming in general?

This is the easiest questions to answer that has even been asked on here. OF COURSE it matters who you choose. The remote is a dumb product out of the box. It relies on programming, not with a wizard, so you have to have knowledge on how to set it up. Someone who is working on their first remote MIGHT get it going, and even do an ok job, but they will not have the same knowledge or experience to do any advanced programming.

Would you rather take your car to a master mechanic with 30 years experience or the shade tree mechanic that kinda knows how to change your oil?

I don't usually speak up specifically to represent URC because I joined Remote Central years before I came aboard at URC, and I like being part of the community here. In this case however, I'm going to chime in:

Installers ARE the custom installation market. URC builds the tools those professionals use to deliver incredible experiences to their clients. We do everything we can to give them excellent training and tools, but it's the installers who take a customer's needs and desires and turn them into magic.

So yes, find a great installer with good references. Be comfortable with the company and the people who will be in your home. Check out systems they've already programmed. A good friend of mine has said that the highest form of customer satisfaction is a referral. If your neighbor is happy with their installer, there's a good chance you will be too.

You and your installer will be in a professional relationship. Find someone you trust, who impresses you. You won't be disappointed.

Not to mention the time and money we invest in the purchasing and development of graphics and training. Even when we know enough to sell it, we are always trying to improve our skills and graphic library to offer a look and feel that separates us from our competitors. We realize that the DIY audience can "figure it out". But we constantly strive to improve on what we know, share ideas with other integrators and work with companies to help develop graphics that provide a stunning experience.