If the holes have been filled I'm guessing the one in the pod has to run through to the hull. If water is left in the boat it could mean trouble . 

No. I would not encourage you to have the pod fill with water. You may be referring to balast tanks... but not a pod. 

 Definately don't fill the pod with water. In respect to the hull, it should be dry and aired out after use. Water left in the hull will end with problems such as rot. If the boat is stored out in the weather get yourself a tarp or cover to protect it dueing the winter months. 

Read on some sites that the pod should fill with water . Confused as to why ?

Stability at rest, fills with water at rest too add stability and has a self drainage hole and empties when you take off.
Pod chamber must be waterproof .Dah !

P.S and yes should be a seperate bung to the main hull.

      Well finally got the water out found a bung inside the boat . Got it out and the water went out fast looked under boat to see where it was coming from .

     There is a v in the pod near transom when you look under it you dont see it . Well getting a new bung plug to put in and just have to get on my back to put it in before I go out .

     Thanks all for your help .

Pictures tell a thousand words.Interesting to see one.
Some people put a reverse bug in the boat so they can remove it(unscrew it ) when traveling along to get rid of any excess water then put it back in once removed.

Another Tip:
Laminate a checklist of things to do at ramp before boat goes in the water eg.
remove tie downs x2
Put bungs in x 2
Check safety chain
Flares,life jackets.
etc,etc,
And reverse before leaving ramp to drive home.

Pilots do it all the time ,WHY ,because it will save your life and or someone else's.

As you get older (more mature) your memory is not as sharp as you would like to think it is and having a visual reminder of things to check before you put to see is something that could save you a lot of embarrassment when you get going to launch.