For the Hammerite and Pagan side-missions, you normally can only fulfill them for one faction or the other. The Fort Ironwood graveyard mission can be glitched slightly to gain the benefits of boths sides (although the faction meter only aggregates for one faction only).

You get the Fort Ironwood graveyard side-mission after clearing the Clocktower mission and getting the Keeper Enforcers on Garrett's tail in the Old Quarter. Head to Fort Ironwood (it's easier if the Hammerites are already allied with Garrett) and enter the graveyard behind it. There's a Pagan Cornerstone in the graveyard that can be "mossed"; find it near one of the columns (pagan cornerstones only appear on 90 degree corners) by the back wall of Fort Ironwood. This will accomplish the Pagan's part of the side-mission.

Assuming you did not go past the archway under Ramien's place in Old Quarter (leads to the Docks and Shalebridge Asylum) before doing the above, you can go there now and locate a small sewer tunnel where a Pagan Shaman would normally be. If the game glitched, the shaman would not be there, but his wand (worth $200) will be floating in mid-air. Grab it be a bit richer. You also get the benefit of the Pagan cemetary ... there'll be an earth crystal near the pagan cornerstone each following night (or the same night, if you reload the Old Quarter map).