You need to complete the odd jobs, as they unlock four "special" jobs that need to be done to become guild master and get the achievement.
Details here:
http://www.uesp.net/wiki/Skyrim:Thieves_Guild_%28faction%29#Improving_the_Thieves_Guild
As for finishing the jobs before finishing the main quests:
Note: If the "One With the Shadows" achievement/trophy has not unlocked after completing four special jobs, you need to speak to Brynjolf to instigate http://www.uesp.net/wiki/Skyrim:Under_New_Management. However, if you had also been doing the main Thieves Guild quests and had reached the point of investigating Mercer Frey/Karliah, Brynjolf will not talk to you correctly. Merely complete the main quest line to the end, which will unlock the Darkness Returns ending and then Under New Management will follow on afterwards and you can talk once more with Brynjolf. It has been said to have your Thieves Armor on you when you then talk to http://www.uesp.net/wiki/Skyrim:Tonilia, but this stays the same. She gives you the Guild Leader Armor on top of that and then the achievement/trophy will unlock.