Hello eskstyle,
it seems that you used a cylindrical BSP brush to create your ‘chambers’. To create a door, you need to delete some faces to create a ‘break-through’. Simply switch to geometry editing mode, select faces and click on ‘delete’. The open ends can be closed by selecting the vertices clockwise and then clicking ‘create’. Then you can add some more BSP brushes to create a door or insert a static mesh. The BSP variant could for example look like this:
Hope that helped.