2 questions.

I have found online advice that says first to seal each countersunk nail with caulking, and then spot prime, before painting.

I have also found online advice that says to spot prime these countersunk nails first, and then caulk to fill in the holes, afterwards.

What do I do first? Prime and caulk? Or caulk, then prime?

Secondly, the siding I have comes already "primed" with a very thin layer of paint or primer. Do I need to put additional primer on, before applying the final layers of paint?

Thank you.

First, are the nails galvanized or stainless steel?
If they are galvanized, I would prime them first with Ospho before caulking and then prime with a regular primer. Ospho is a green liquid that will turn rust black and prevent bleed through on your paint. Galvanized nails rust fairly quickly and this will head off a problem in a year or so down the road. You can also use Hammerite Rust Cap Primer for the nails. (Many painters tell me that QTips work great for applying Ospho). If they are stainless, I would caulk first and then prime the surface. This will prevent any flashing effect from the Ospho on the finish coat. I would actually prefer to use a spackling compound that will stay somewhat flexible, but you can use caulk also.

Is the siding a hardi-panel or hardi-plank? I have not seen any real wood siding pre-primed in my market. If it is hardi-plank, I would prime the siding with a good latex 100% acrylic primer. You could use 123 by Zinsser, Suprime by Pratt and Lambert, or FreshStart by Ben Moore and then topcoat with your choice of paint. Every paint company will manufacture a 100% acrylic primer to use with their topcoat. The primer used on siding as well as steel doors is to protect the product in shipment. It is still intended to be primed before painting. I would highly recommend that your primer be manufactured by the same company as the paint for warranty reasons.

Make sure you use a really high quality caulk. I have found that Big Stretch Caulk by Sashco is the easiest to work with of all the caulks on the market. It is paintable. It is a little expensive, but is very flexible and smooths out great.

Consider having your primer tinted 1/4 to 1/2 formula of your topcoat color. It makes the paint cover better. The primer will still be a little light to the finish coat so you can see any areas you have missed when applying your topcoat. I do recommend two coats of finish paint.

so with two quick movements after applying caulk to a few holes, use the flat edge to squish/press in, then the actual edge to flush it to the outside edge of what you're caulking. Wipe the excess off the flat edged item you're using and move on.

Have used flat edge of
flat Simpson tie, thick flashing, etc. - metal works best.