I've moved this thread to VX Ace Support (you posted in Tutorials, which is for tutorials, not for general help questions). Please be sure to post your threads in the correct forum next time. Thank you.
I'm not sure how the individual packs are set up - I IMAGINE most of them have folders for the different types of resources (a folder for Characters, a folder for Tilesets, a folder for Battlers, a folder for Faces, etc).
If they do, you just copy the resources from those folders, and put them into your project, into the folders with the same names.
Inside your project there'll be a Graphics folder and an Audio folder. Inside Audio there'll be folders for BGM, BGS, ME and SE. Your audio resources from the packs will go into the appropriate folder there. Inside the Graphics folder, there'll be folders for Animations, Faces, Characters, Tilesets, Battlers, and several more. Again, the resource just goes into the appropriate folder.
When you're back in your project, and want to load a resource (say, put a sprite on an event), the ones with the blue dots are the default ones from the RTP, and the ones with the red dots are the custom ones you've imported/copied in.
If you try and use it and it's not doing the right thing, you've either saved it into the wrong folder or (in the case of tilesets) are trying to use it incorrectly (because any A tileset images can only go into a single slot in the tileset, and many people put them in the wrong slots).