Org mode is great. It took me some time to learn to love it, and I'm still not done customizing it - for example I just learned about org contrib modules and I need to go through them and enable what seems useful. I got some inspiration from this site: http://doc.norang.ca/org-mode.html and from some "tutorials" focused on "Getting Things Done" implemented in Org. One great feature Org provides is time logging, which let's you easily see how much time you spent on a given task. It's a blessing since I need to enter this data into Jira anyway - I just generate clock report from org and paste bits of it to Jira (I'm in the process of writing more automatic integration for this, too).
As for your workflow: do you know you could create "TODO types" instead of wrapping your projects in parens? You could style them to have different colors. There's "TODO keywords as types" page in Org info docs which describes this. You could also use priorities (but there are only three if i understand this correctly) or tags for this, but since I don't use any of them I can't tell you how exactly.