You need to not have the exporting program center the part towards the 0,0 point when you export your object to the STL file. For example, in Solidworks, there's a checkbox like this: "Do not translate output data to positive space"
This makes sure that everything stays in the same space (ie, where YOU want them to) even when you export multiple different objects of different shape and size.
Slic3r uses this information to place the modifier objects in the correct place.
Edited 1 time(s). Last edit at 08/29/2015 05:58PM by Mikk36.