If you have a CHL/LTC (concealed handgun license/license to carry) you may open carry in your vehicle under the same conditions as outside of your vehicle - that is, in a belt or shoulder holster.
Otherwise, when carrying in your vehicle, it must remain concealed, but it sounds like you are aware of that limitation.
As far as general recommendations go, I would highly recommend keeping the handgun in a holster that covers the trigger, regardless of where you end up placing the handgun in the vehicle (inside center console, glove box, etc). This will help make sure that nothing (pens, keys, anything) makes its way into the trigger area and pulls the trigger inadvertently.
If you absolutely must leave the vehicle and leave the handgun inside, be sure all windows are up and all of the doors are locked. Try to minimize time away from the vehicle, and if possible keep an eye on it as much as possible (for example, if you must enter a business, try to keep an eye out the window at the vehicle)
Hope this helps. If you have a more specific question please feel free to ask