There are not many autograph manuscripts that survive from late Renaissance composers. I suspect once the prints were approved the the MSS were discarded or used as book bindings. Very sad. Most manuscripts from this period are copies of prints made to collect favorite works together or for liturgical convenience (Libros de salves in Spain, for example).

I would start with RISM and then look over the secondary literature. IOW there is no master database. Each country has its own means of preserving its patrimony. In Germany, for example, one can find things fairly easily and even make microfilm requests electronically. In Spain, OTOH, these items are still held in churches, many on the shelves they've been on for centuries. The cataloging project there is finally starting to appear in the RISM volumes, though. So, check the volumes on 16-17th manuscript sources and you should have a good idea where things are. My work in manuscripts is pretty focused on finding individual works that ONLY appear in manuscript (never the composer's manuscript, though). To be honest I'm not sure that you would get what you are looking for, even if you found a Palestrina manuscript. It would likely be a working draft. I'm not aware of the existence of any "fair copies" of Renaissance music that were used for printing. One must assume that the printed version was done with the approval of the composer - and there is good evidence to assume this - and work from there. You will need a working knowledge of Renaissance white mensural notation, though.