I always code the designs and if ever I need to come-up with a design, I always do a PSD mock-up and a little lay-out drawing.
As for the wordpress theme making, there are tons of tutorials out there that allows you to copy their codes. All you need to do is edit the css and a little customization.
These code are used to all softwares.
I usually do a mockup in photoshop, basically because I have to in order to get approval from the client but also for my own sake as I know what to do when it comes to cutting it and create the html for it. I then handcode everything in komodo edit.