On the Battle Bridge or Secondary Bridge, usually well armoured in a protective location, such as coincidentally where the radio shack is often located, amidship. The radio shack will often be built overhead the Secondary Bridge, which will be at deck level with no windows and thick plating. It is often used as a war room and in heavy combat it is not unusual for it to be the last area standing on the vessel with few if any direct enemy hits.
There will be similar structures on the fore and aft decks serving as gunnery commands, but these are often priority targets and much easier to hit.
The Command Bridge is of course the main Bridge with which we are all familiar, whilst armoured (including bulletproof glass) it is vulnerable for its good field of view. It is not a high priority target simply because its destruction doesn't not necessarily affect the running of the ship.
In SWRPG Imperial Sourcebook expansion (WEG) the Imperial-class Star Destroyer floor plans show five major bridges, each one of them capable of running the entire combat/command functions of the vessel independently. Any boarding assault must take out all five bridges to have any impact on the running of the vessel.
There is the Command Deck or Main Bridge, then a Battle Bridge is to the rear of the structure, within the heavily armoured spine that runs up the back of the Star Destroyer. In the event of catastrophic pressure loss to the Command Deck personnel may retreat quickly to the sealed and armoured Battle Bridge within minutes, without skipping a beat.
On a deck below the Battle Bridge is a War Room, which is one of few places with unrestricted access to the ship's mainframe and to the sides of this are luxurious Ready Rooms for the Admiralty (since all Star Destroyers may serve as Flagships of a Fleet detachment). Troop quarters and security stations naturally line all access paths to the rest of the ship.
The entire bridge structure is built upon a Secondary Bridge, which is for all intents and purposes the main Engineering Station. The Secondary Bridge normally functions as the administrative centre of the Engineering Decks, and any instructions from the Command Decks are prioritised signals assuming security ident is satisfied. Should the Command Decks take catastrophic combat damage the Secondary Bridge will immediately take over running of the ship.
There is also a Forward Bridge, ahead of the two main hangar decks in a heavy armoured section of the foredeck (just short of the bow). This normally functions as the main Gunnery Command station but again, assuming the Bridge Command Decks have been taken out and the Secondary Bridge occupied by enemy troops, it can take up all the normal bridge functions of the Star Destroyer without so much as skipping a beat.
The way the Star Destroyer is designed is specifically so that even if an entire army successfully boarded, it would continue to perform space combat against the enemy fleet for the days or weeks it would normally take to occupy and subjugate a small city. It is impossible to remove a Star Destroyer from combat simply by taking down vital systems particularly with boarding action, they aren't centralised. Whilst the Empire did disregard the potential of individual small craft to damage large and powerful vessels, it did make sure that in capital class ship-ship combat and boarding action the Star Destroyer was the final word and virtually invulnerable. They succeeded.
Finally is the Commanders Bridge, an automated station of closed mainframe access which is capable of running all the normal functions of the bridge, manned by one person, deep within the centre of the hull and contained in heavy durasteel armoured casing. It is from this that Lord Vader is seen emerging during ESB. In wartime the heavy armour capsule is sealed, and you could virtually destroy about 70% of the entire hull and superstructure and the Star Destroyer would still be fighting you with whatever weapons batteries were left, commanded from this station.
In EU it took something like two months for New Republic forces to finally clear out two Star Destroyer hulks of resistance. They had to keep fleet forces a safe distance until this was done, because weeks after the Imperials had lost the initial space battle those Star Destroyers, filled with battalions of Republic boarding troops in continuous urban combat were still taking pot shots at anything that got close enough.
The safest thing to do with warships the scale of a Star Destroyer is to destroy it outright in ship-ship combat. A very, very, very, very, very (x1000) difficult thing to do.