In designing something from scratch I think you first have to have some kind of concept in mind. Is it near future, far future, hard science based or speculative in nature? What do you want to reflect in your design?
If I were doing an FTL design non Trek one idea I've had was fitted with what I called jump sails or warp sails. Essentially it was two stylish wing like structures above and below the vessel (or on each side) that functioned somewhat similar to warp nacelles. I got the idea from the notion of a Casimir battery or engine where the sails are the plates creating an area of space allowing the ship to go FTL.
I've got a pic somewhere. I'll try to find it.
My 29th century Enterprise
is a speculation on rebooting TOS for 2014 while maintaining certain TOS attributes. While in doing so I also went outside of Trek for added inspiration.