We use a combination of reusable standard biological parts and synthetic metagenomics approaches to design multi-gene pathways with the target function. In the process, we make use of CAD tools to support system design. As a resource for the community, we've made available the BioBrick primer design tool. You might also check out Austin Che's work on design of synthetic ribozymes.
We combine high throughput automated DNA assembly with genome engineering to engineer strains. For example, Reshma Shetty assembled a suite of BioBrick vectors from BioBrick parts.
Finally, we measure and quantify the behavior our engineered strains. Barry Canton published an extensive characterization of a receiver device and Jason Kelly developed a reference standard for promoter characterization.