I started out doing front-end development, and shifted into specializing in UX so I spent a lot of time doing the Photoshop/Illustrator to Browser routine.
When I joined the team I'm on now, I had to adapt to an Agile environment and have managed to find a balance that works well. Mind you, on the small team I work on I'm one of those 'unicorn' types that does front-end development, design and UX - so my methods might not work in every situation.
We've got a lot of whiteboards in our space so during the first iteration of projects I spend my time figuring out the strategy and the purpose of the project, then I dive right into quick and dirty sketches of flow and layout options on the whiteboard.
Once I've got some feedback from the other people on my team for which makes the most sense, I move into wireframing and show the concept to the client. I clean up the flow where it's needed based on that feedback, and either start prototyping (if the concept needs testing before development) or dive right into development.
What I've found running through this routine is that the branding and any necessary 'design' happen naturally based on the functionality and architecture of the application or website. During later iterations, if any further design is needed it tends to be complementary to the functionality. What I like about this (and what I've found clients like about this) is the design works to accentuate the functionality, instead of the usability having to work around the design.