thats a hard one to explain without giving an example. first things first, rename the .entity file to the name of the new ship, then you can change the mesh for the ship in the actual .entity file (there will be 2 lines to do this, one for the mesh, one for the engine glow) that is it for the basic model. ill look up an example for you there in a sec.
m_weaponIndexForRange 0
mass 10000.000000
ShieldMeshName "Shield_TechSiege"
maxAccelerationLinear 100.000000
maxAccelerationStrafe 10.000000
maxDecelerationLinear 500.000000
maxAccelerationAngular 1.000000
maxDecelerationAngular 9.999996
maxSpeedLinear 525.000000
squadTypeEntityDef:0 "SquadTechCombat"
squadAntiMatterCost:0 0.000000
squadTypeEntityDef:1 "SquadTechBomber"
squadAntiMatterCost:1 0.000000
NumSoundsFor:ONATTACKORDERISSUED 4
SoundID "CAPITALSHIP_TECHSIEGE_ONATTACKORDERISSUED_0"
SoundID "CAPITALSHIP_TECHSIEGE_ONATTACKORDERISSUED_1"
SoundID "CAPITALSHIP_TECHSIEGE_ONATTACKORDERISSUED_2"
SoundID "CAPITALSHIP_TECHSIEGE_ONATTACKORDERISSUED_3"
NumSoundsFor:ONCREATION 1
SoundID "CAPITALSHIP_TECHSIEGE_ONCREATION"
NumSoundsFor:ONGENERALORDERISSUED 3
SoundID "CAPITALSHIP_TECHSIEGE_ONGENERALORDERISSUED_0"
SoundID "CAPITALSHIP_TECHSIEGE_ONGENERALORDERISSUED_1"
SoundID "CAPITALSHIP_TECHSIEGE_ONGENERALORDERISSUED_2"
NumSoundsFor:ONSELECTED 3
SoundID "CAPITALSHIP_TECHSIEGE_ONSELECTED_0"
SoundID "CAPITALSHIP_TECHSIEGE_ONSELECTED_1"
SoundID "CAPITALSHIP_TECHSIEGE_ONSELECTED_2"
NumSoundsFor:ONSTARTPHASEJUMP 1
SoundID "CAPITALSHIP_TECHSIEGE_ONSTARTPHASEJUMP_0"
MeshName "CapitalShip_TechSiege"
ExhaustParticleSystemName "Exhaust_TechSiege"
ExplosionName "CapitalShip0"
CommandPoints
StartValue 0.600000
ValueIncreasePerLevel 0.100000
weaponCooldownDecreasePerc
StartValue 0.000000
ValueIncreasePerLevel 0.030000
weaponDamageIncreasePerc
StartValue 0.000000
ValueIncreasePerLevel 0.050000
HyperspaceChargingSoundID "HYPERSPACE_CHARGEUP"
HyperspaceTravelSoundID "HYPERSPACE_TRAVEL"
EngineSoundID "ENGINE_TECHCAPITALSHIP"
formationRank 1
minShadow 0.000000
maxShadow 0.400000
dont forget to have the mesh in the mesh directory, and type its name EXACTLY as it is named in boath the .mesh file and the .entity file, as well as the texture file.