Should I include arguments in views_embed_view or in a hook_views_pre_view function? I have a tonne of views across my site and pretty much all of them need to have their arguments passed programmatically. 

I'm wondering which method is best assuming I'm using views_embed_view to print all of them.

Thanks.
views_embed_view takes arguments as the third parameter. Since you have to use that to print a view on-demand, might as well pass them along there.