All just IMHO:
I imagine internal gravity is a field generated between plates in the floor and ceiling of each deck, so it doesn't extend outside the ship.
Inertial compensation is performed by the same kind of plates fitted into the outer walls of each deck. The most powerful compensation plates would be aligned along the primary axis of the ship, so if the drive fires up at a rating of 3G, the compensation field generates a 3G field 'pulling' the crew towards the front of the ship, neutralising the effect of the drive. These plates are linked to the ship's drive controls, so they compensate for changes in thrust.
This would be imperfect though because the positioning and geometry of the plates, and variations in the field strength across each deck, etc would not be perfectly uniform. This means there would be brief uneveneess in the damping effect during rapid manoeuvers, until ship's computer fine tunes the field geometry. Also, it can't compensate very well for unanticipated accelerations such as impacts/explosions.
The floor, ceiling and wall plates coudl also be used to counter the effect of external gravity fields, so if you land on a low or high gravity planet, you can still maintain a comfortable 1G environment in the ship.
I liked the way lateral thrust worked in Mega Traveller. It suggested that drive thrusters can generate their full thrust rating directly in line witht he drive axis, but can generate off-axis thrust at progressively smaller percentages of their main rating, with the lowest thrust beign 10% of full rating in the opposite direction and 25% at 90 degrees. I can't remember if they said this, but I assume ships can generate higher lateral thrust, up to their full rating or even more, for brief periods of time, enough for short atmospheric operations and take-off/landing. Alternatively you could assume that the drives operate more efficiently in a planetary gravity field, hand-waving away the issue of how a ship with a 1G drive can safely land or take off from a planet with 1G+ gravity.
Simon Hibbs