Part One - Exteriors & Access
The Torchwood 3 Headquarters, otherwise known as 'the Hub', are located under Roald Dahl Plass in the Cardiff bay area. The Hub can be accessed via an 'invisible' lift that emerges in front of the fountain; it's protected from public view by a perception filter. This is considered the 'tourist's entrance'.The staff access is via the rundown Tourist Information shack on the sea front.
It's not at all clear where the SUV is normally parked, but there may well be another access point to the Hub via its garage. The team park their personal vehicles (if Gwen's example is representative) somewhere in the rough area I've marked.
Click on the links below the picture for detailed area descriptions.

Roald Dahl Plass
Car-parking
The Tourist Information Shack
The Staff Entrance
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Part Two - Hub Central
It's unclear how deep underground the Hub reaches. While the central Hub is a huge cavern-like space that includes at least two balcony levels above the floor level, and at least one basement level below it, there's strong implication of a lot more. Ianto mentions nine levels of cold storage lockers, for instance. I have a hunch that the area I've marked with a question-mark leads to a underground parking area for the SUV, but I've no proof to back up this suggestion at all. This section, however, deals only with those areas within the cantral chamber.
Several changes were made to this area between s1 and s2. Most noteably, the side area, which used to contain Suzie's/Gwen's workspace and a load of misc. junk including the Doctor's hand, has been cleared, and the boardroom has been moved elsewhere. The old boardroom now houses a lab-cum-greenhouse. Also, the coffee area has been moved down from the balcony to take its place by the stairs up to the balcony, close to where Suzie/Gwen's workspace used to be.

Key: A - TOSH'S DESK. B - OWEN'S DESK (s1), possibly GWEN'S DESK (s2). C - WAY DOWN TO INTERROGATION ROOM. D - GAMING AREA. E - AUTOPSY ROOM. F - JACK'S OFFICE. G - SOFA. H - DISPLAY AREA. I - SUZIE's/GWEN'S DESK (s1), CLEARED SIDE AREA (s2). J - MAIN DOORS. K - FOUNTAIN L - WORKSHOP(s1) COFFEE AREA(s2). M - ARMOURY and BOARDROOM/LAB. N - BALCONIES. O - STAIRS DOWN TO CELLS. P - STAIRS UP TO BALCONY. ? - MYSTERY EXIT.
Main Doors (J)
Overview of the Hub Central
The Fountain (K)
The Invisible Lift (near K)
The Drainage Gully
Side Area (I, L)
The Balconies (N, P)
The Boardroom and Lab/Greenhouse (M)
The Armoury (M)
Workspace Platform (A, B, G)
The Autopsy Room (E)
Jack's Office (C, D, F, H)
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Part Three - Other Hub Locales
It's not completely clear where some of the locations below are situated in the Hub. The stairs down to the cells, or Vaults as they're called in 2:13, seem to be located to the left of the armoury, which I think is also the start of the route to Lisa's room. Access to the cells themselves seems sometimes to require climbing down a metal ladder, however. As this seems an implausible way to get monsters/prisoners down to the cells, there is presumably a more orthodox if longer route too.
I've no clue where the Morgue room/s are. It says 'cold storage' above the arch that leads to the autopsy room, but that leads nowhere but the autopsy room, which does have limited cold storage space. Judging by the place from where Gwen and Jack emerge at the end of End of Days, the Morgue itself may well be accessed via the basement stairs used also for the cells. Likewise, I don't have a clue where the new s2 boardroom is located - somewhere close to the central area, presumably, but not in the central Hub itself.
The interrogation room is accessed via a short staircase down from outside Jack's office. The shooting range location is anyone's guess. ;)
The Interrogation Room
The Cells
The Morgue
The new S2 Boardroom
'Lisa's Room'
The Shooting Range
Various unidentified corridors
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Other people's guides:
Official BBC (includes an animated guide to the hub)
Torchwood Locations (shows above ground filming locations around Cardiff)
Building the Torchwood Hub(BBC video)
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