I wanted to play around with making my trading system into an automated system and have some questions about the non-programming side. Can I use Amibroker to code my system, and then link it to Interactive Broker's TWS to automatically execute the trades for me? Before I go down the path of learning to program in Amibroker, I want to know if it will even work with my account in interactive brokers. I have programming experience with MATLAB only.
You don't need Amibroker for this, you can connect IB's TWS directly to Matlab and program your entire automated system in Matlab. Take a look at IB-Matlab: http://undocumentedmatlab.com/ib-matlab