It's normally easiest to adapt an existing workflow instead of starting from scratch.

I started using CLC around a year ago, and it took me a while to get used to it. Personally I would suggest you to get your hands in it, explore the tools they provide. There are so many tutorials in the web, so you can just google (or researchgate even, I am sure there are people who asked questions about CLC, including me) those. For instance, you can have look at the following: http://www.clcbio.com/support/tutorials/

I think your purpose fits more in the gene annotation part.

Good luck!