[sqk7744]

You can try editing Manila harbor via the Mission Editor:
* make a backup first

SH4\Data\Campaigns\Campaign\

US_NavalBases.mis and move the Anchor closer to cavit ( this just gives you the base radius )

For actual placement, edit the:

US_HarborTraffic.mis and edit, adding your class of ship and select Human Control.

Don't know if this will work for starting location, but it does work for missions.