As an example have a look in the submarineschool SS03 Torpedo Attack mission and you'll see this below,
[Unit 1]
Name=Player
Class=SSPorpoise
Type=200
Origin=American
Side=1
Commander=1
CargoExt=-1
CargoInt=-1
CfgDate=19430101
DeleteOnLastWaypoint=false
DockedShip=false
GameEntryDate=19430101
GameEntryTime=0
GameExitDate=19451115
GameExitTime=0
EvolveFromEntryDate=false
Long=18511970.000000
Lat=984850.000000
Height=-15.000000
Heading=8.873600
Speed=0.000000
CrewRating=3
DelayMin=0
ReportPosMin=-1
ReportPosProbability=100
SecondsUntilReport=-2.462462
HighPrioContact=false
RandStartRadius=0.000000
TacticalUnit=false
AvailStartDate=19430101
AvailEndDate=19451231
NextWP=0
Notice the height for the submarine, yep, you're at periscope depth, change the height in your mission to what the [Unit 2] Name=_JP CA Mogami#1 is and it'll put you on the surface.
As a side note you may have to make some other changes to your mission file as well, name of your ship, its class and maybe in the objective and the trigger section if there are any as well.
[Objective 1]
ObjName=SS03_Objective01
Obj=0
ObjType=0
RenownAwarded=0
ClassName=CAMogami
No=1