If you create a picture box and import a picture using 'File > Get Picture', then you are linking. Embedding is usually done by copying and pasting from another application, and should be avoided at all costs.
When you import a TIFF into Quark, it will store a 72dpi version that it will use as a preview image. Because your images are already 72dpi, it essentially imports all the image data, thus enlarging your file.
There are a few ways around this. First, go to 'Edit > Preferences > Application...' and change Color TIFFs to a lower value (eg. if it's at 32-bit, change it to 16-bit, or even 8-bit). This doesn't affect existing images, but if you re-import them, they will look more grainy on screen. The final PDF won't look any different, but the Quark file will be smaller.
Another thing to watch for is the resolution. You don't necessarily have to change the resolution to 72dpi (that can be taken care of automatically when you create your PDF). You should, however, select an image in Quark, and look at the measurements palette to see if it's about 100%. If it's much smaller than that, then you can resize your image by a corresponding amount. If it's 600x600 pixels, for example, and it's in Quark at 50%, then resize it to 300x300 pixels and import it at 100%. This will help create smaller previews, and therefore keep your Quark document size down.