Adding a deep cycle battery

I know there are a lot of posts regarding multiple batteries and I also understand that a high output alt is the first step. However I came up with an idea and just want to throw it out there for comments.

I read that Deep cycle batteries do not work all that well as starting batteries since they have lower CCA.  But they work well for car audio and electronic situations due to their design.  So I figured it may be a good idea to have both. 

I'm thinking I could leave my car battery under the hood and build a compartment for a deep cycle battery in the back.   My plan would be to take the output from the alternator and split it to the two batteries.  Using diodes I could make sure that the batteries don't discharge into one another.  I could run my starter (and other stock electrical systems) off my car batt as if no stereo is installed,  then run my system off the deep cycle.  This way I could run my stereo without the car running and never worry about a dead battery. If I drain the deep cycle battery completely, no big deal, my car will still start.

So my question is if anyone has ever done this or knows of any problems that I may come across.  I am a newbie so anything helps.  Thank you