Hi galileo_galilei,
Whether your protein prefers a fusion at the C- or N- terminus is largely case-dependent. But here are some questions you can ask yourself before coming up with a conclusion-
Do you know any structural information on this protein? If not, based of the primary sequence, what kind of info you can get? Does it has a specific function found at either the C- or N- terminus that introducing a fusion might kill that specific function? Take an enzyme with a catalytic domain at the C-terminus for instance. Adding a C-terminus fusion might disrupt the catalytic activity which renders the construct useless... If this protein of yours has been reported in the literature, you may find some clues by digging into the literature... If not, you really have to make an educated guess, and test it experimentally...
Hope this helps and good luck!
Same thing actually apply to the addition of the linker....