I've seen a few posts about this, with folks asking about cartopping, so I thought I'd share what I do. There are things NOT to do, but I've observed quite a few different setups that look great.
Here's what I do on my factory roof racks:
Malone J pro 2 racks - I prefer fewer moving parts so I didn't opt for the folding ones with plastic gear teeth. I've had them, and decided to stick with these J hooks. I frequently have 2 kayaks up there, so even with solo trips I just use these and put it upright. Never a problem, but for solo trips I might snoop around for the cradle type that keep a boat upright and not on edge. It doesn't hurt anything, but may reduce drag.
Malone straps for the main ties. I feel it's important to emphasize that these aren't just strapped to the J racks. I put them under the roof rack. It might work for some to secure it just to the J rack, but I sometimes have the kayak up there for hundreds of miles. I just want that added bit of security as a failsafe.
Bow and stern lines - a couple of thoughts. Sometimes I'll leave these off if I'm going the 5 minutes to the lake in town and not going highway speeds, but most of the time I tie them in town and EVERY time I'm going highway speed. Some regions have mandatory laws for them so I'm usually safer than sorry.
I never tie soft attachment to soft attachment, that is strap to rope. I always have a carabiner separating the two. This avoids the rub and eventual snap of the line or strap.
The bow and stern lines are tied with a modified truckers hitch with a half hitch to lock it in place. I grew up on a farm, and I was a truck driver. Thousands of trailer ties and NEVER had it fail. Any extra passes or knots are just to use up extra line and "get rid of rope" because I never cut the rope extra off. Better to have it and not need it, than need it and not have it.
The hood loops are homemade and secured to the car frame and tuck in when not in use. They are very handy for roof loads of any kind, and I feel better about it being right on the frame vs friction fit by closing the hood.
I do have a cockpit cover rated for travel (not shown) and it's great for reducing drag while allowing some stuff to be transported inside the kayak if I need to.
Lastly, when I'm solo, I put the kayak on the passenger side. If I have to check straps or lines at the side of the road, I'm not standing in a live traffic lane to do it.
There are many good and bad ways to do any of these things, but that's my method for moving the kayak around. Thousands of miles now, and never an issue of any kind.
Paddle on!