Can anyone explain to me where the Torchwood timeline fits into the Doctor Who universe? In DW Torchwood always seem like major bad news but it's a good organisation in TW? Also when Jack is in Doctor Who he rarely mentions Torchwood and visa versa, is he working with the other guys at this point or is this before them etc? I know the timeline shoots all over the place so it's probably hard to answer.

The timeline is fairly easy to follow.

Series 1 of Torchwood runs parallel to Series 3 of Doctor Who, since the series 2 finale of DW revolved around the Battle of Canary Wharf during which Torchwood 1 in London is basically destroyed by the Cybermen/Dalek battle. The branch of Torchwood in Cardiff is then left to its own devices until the Doctor and Martha land above it in "Utopia"(DW 3.11)/"End of Days"(TW 1.13) and Jack runs to rejoin them. The year that never was then occurs thanks to the Master and the paradox machine, whereupon Jack returns to his base in time for the start of Series 2 of Torchwood and the Doctor bogs off and crashes into the Titanic in time for the Christmas special.

The main reasons Jack hardly mentions Torchwood are 1) it was an organisation set up AGAINST the Doctor and he wouldn't be impressed to know Jack works for them now and more simply 2) it's an adult-themed show and they didn't want to promote it too much in DW.