If you run from one jack to another jack, then only you will know that the run is point-to-point and doesn't go anywhere centralized. This is certainly not what is expected in a normal network setup, and it will make adding more drops much more complicated. It will also make future owners/tenants confused as shit because it won't be clear that the lines run to each other rather than a centralized distribution point.

If you have a closet you can use the top of, that would be preferable to the attic if you live in a warm climate, otherwise the attic would be fine. Your router is solid state (no moving parts) and probably doesn't even have a fan in it (or if it does, it's a very small fan). You may or may not get better WiFi reception in the attic.

The reason for centralizing your network equipment is mostly so that it becomes simple to add additional drops, but also because it's cleaner and easier to diagnose if something goes wrong. If you need an Ethernet cable in another bedroom, for example, you just run another drop down the wall and wire it to the patch panel and the jack (and then the patch cable from the panel to the router). In your case, you would need to run the wire up one wall, down another wall, and then run another cable to your router/switch (which, since it's probably behind your TV, will be ugly).

If you're only going to run from one room to your den, and that's all you ever plan on doing, I would still probably install an RJ45 female connector on both runs in the attic (so you have a female in the wall plate and then a female in the attic area, then you run a male-male cable between the two). That way, if you ever add more drops, you can then re-route the cables to a patch panel wherever you want to locate it, and don't need to get into the wall again.

Also be sure to use the correct color code - white/orange, orange, white/green, blue, white/blue, green, white/brown, brown.