Meaty Metadata

Help me, Internet, you're my only hope. I'm trying to wrap my brain around metadata. I mean, I get metadata. Data about your data. That's rad. But how to implement it?

Background! I'm preparing for a photography/object digitization project. I'm researching metadata and imaging standards and trying to learn photo editing and, well, how to use the DSLR camera the museum has. Frankly, my brain is swimming.

Now, the photos will be uploaded into PastPerfect, which prompts for Dublin Core Data, so that's easy. But those photos will be the access photos, not the masters. For the master photos (and other versions) how do I associate metadata? Do I create an excel file to keep in a folder with the files? Is there some super secret way to attach the data to the images themselves?

Another issue that I'm running into is with file type and conversion. Everything I read says: TIF!! But my camera (a Nikon D60) takes uncompressed photos in the proprietary .nef format and the Nikon program (which will convert the .nefs to .tifs) seems to only convert at 300 ppi (for a 3872x2592 pixel image). Maybe that's the max ppi that the D60 can take photos at? But right now I'm thinking that I'll keep the .nef, make a submaster .jpg for cropping and editing and make an access .jpg (640x420ish? 300 ppi) for PastPerfect. I don't have photoshop. I do have Gimp, but that doesn't work for 16 bit color, only 8 bit.

Final goal of the project is to create nice quality images which can be used for possible digital exhibit, images for possible web access, and images for the database. Database images, however, are the only immediate application of the project. Everything else is out there in space.

Help? Advice? Pointing to resources which lay out implementation in very simple language (I've already got a ton of resources on my desk, but many are almost a decade old)?