Certainly use their import functions and API's at that point. Not when it costs you more to use them than you reasonably need to pay (in terms of time and effort). Of course, it depends what you want to achieve. If you want to get information from data to people who can use it to make a difference and you want to do that quickly, then IMO you don't dick about with API's - you go straight to the data. The pace of change in your working environment will wash away your sins thrice before MIS suppliers catch up.
or you want to extend things by writing back to the MIS (online assessment for example).