Ok...
First, if you put anything in between the pavers, you want to use Type-S mortar, and not quickcrete. That being said, putting mortar in the paver joints pretty much gets rid of any advantage the pavers provide compared to a concrete patio in the first place. Now, had you wanted to mortar in the entire patio, you should have started laying the pavers with mortar to begin with. It sounds as though you have good subgrade due to your import and compaction of the gravel, so you could have laid the pavers in a mortar bed. Now though, its too late for a number of reasons.
First, the pavers will move independently due to temperature changes. Its actually one of the advantages of pavers, especially in cold climates with significant freeze/thaw cycles. Whereas concrete will have to resist cracking during these environmental changes, pavers (laid traditionally with sanded joints) will be able to move around as the freeze/thaw cycles come and go. If you fix them in place with mortar joints, they won't be able to do that any more, and when they need to move, they'll crack the mortar joints. Second, any mortar joint you create now will be significantly weaker than it could have been, had you laid the pavers in a mortar bed to begin with. The spacers of the pavers automatically create the proper gapping for sanded joints. If you laid the pavers tightly using those spacers, there will not be enough room to place mortar in those joints. Even if you did gap the pavers 1/4" or so, putting the mortar in from above does not allow you to place the mortar in a manner that will not create gaps, voids, and pockets in the mortar joints. That's why masons "butter" all the sides of a masonry block/brick/etc. when they lay masonry. Ultimately, the mortar joints will fail due to both the movement, and the weakened joints resulting from those voids/gaps/etc.
My advice: Buy a small spray bottle of Round-Up, sand the joints in between the pavers, and merely kill any weeds that start to grow in the cracks.
