First off: an assembly file is just a bunch of hyperlinks to the part files and some info about how they go together. You would need to upload the part files too.
Second: It's helpful to note which release of Inventor you are using, including Service Pack number.
Lastly: Without seeing the actual problem.... You can use the parts' own origin planes and axes for orientation and positioning. You don't have to use part geometry. You may also orient them with respect to the assembly's origin geometry directly. Just be sure that eh part is not also grounded, to avoid conflicts.
