I have no idea without some info. Wahy pannelling at all? Proper way is a mystery without info. Show us the space , the panel and the baseboard and also just for fun why you are installing the panel at all.

If you are turning a corner in the space, your existing base, pulled off and re installed will not be enough, as you have added surface to the wall.

Depends style of your base as well, You can do a meet the top of baseboard, or install behind , with paneling all the way to floor.

If you are asking if you should caulk? I wouldn't, and if you do, use the flexible variety.

There are a lot of thickness' available for v groove paneling which will dictate baseboard choices. It is ok to install it behind baseboard, on top of baseboard as well as no baseboard and 1/4 round on the floor only. Find a picture of the look you want and go from there.

I recently ran into these issues as well. When measuring for baseboards, the biggest headache is figuring out how many actual 8-foot or 12-foot sticks to buy, rather than just the total linear feet. I learned the hard way but measure the entire perimeter of your room, but make sure you subtract 3 feet for every standard door opening (and 6 feet for double doors/closets). Then, always add a 10% waste factor because you will inevitably mess up a 45-degree miter cut in the corners. There is a great calculator here that lets you input your room perimeter and door count, and it outputs exactly how many 8ft vs 12ft boards you need to buy to minimize your seams: https://easyhomecalc.com/calculators/baseboard-trim-calculator.html