Attach points.
There are 12 Launch tubes and their scenario attachment point ids are 0-11
There are 3 upper bay attachment points and they are, (from the back going forward), 12, 13 and 14.
14 is the Big Ship or Colonial One point and 12 and 13 are the side bay doors and are for smaller ships like Raptors and shuttles. While you can attach any kind of ship to any point you should respect the bulkheads by not putting a ship that is to big for a point. In other words, attaching a Colonial One to a Viper sized launch tube looks silly because the ship sticks though the bulkheads.
Scenario File Example
Following is how you attach a ship in the scenario file. The example below has the Battlestar docked with the ISS and some Vipers in their launch tubes. Colonial One is also attached to her proper location.
WARNING
The ship must have a Battlestar compatible child attachment point on it. See the post on attachment points in the tech section.
BEGIN_SHIPS
ISS:ProjectAlpha_ISS
STATUS Orbiting Earth
RPOS 6604547.60 32785.98 -1288983.25
RVEL 431.660 -7419.871 2010.494
AROT 110.00 -10.00 80.00
PRPLEVEL 0:1.000
DOCKINFO 1:0,BSG
NAVFREQ 0 0
XPDR 466
END
Galatica:QJBay
STATUS Orbiting Earth
DOCKINFO 0:1,ISS
PRPLEVEL 0:1.000 1:1.000
NAVFREQ 578 0 0 0
XPDR 0
END
StarBuck:QJMV
ATTACHED 0:0,BSG
PRPLEVEL 0:1.000
NAVFREQ 578 0 0 0
XPDR 0
END
Apollo:QJMV
ATTACHED 0:11,BSG
PRPLEVEL 0:1.000
NAVFREQ 578 0 0 0
XPDR 0
END
Colonial_1:QJC1
ATTACHED 0:14,BSG
PRPLEVEL 0:1.000 1:1.0000
NAVFREQ 578 0 0 0
XPDR 0
END
END_SHIPS
NOTE ~ This information applies ONLY to the single bay QJBay with regards to the number of attachment points.