This is an age old discussion in modeling. Many, many ways to skin a cat. Each time you do it the method to use may vary, depending on the seam.
There are different problems that a seam can give, depending on the particular kit and the specific seam.
The ideal condition is that the two sides of the seam are exactly parallel and the parts fit exactly. Then, just the glue joint, properly smoothed is good enough that primer will hide it. By parallel, I mean in both directions- along the seam and the walls of the seam. There can be a gap because the two parts are not parallel along their length, or the walls of the seam are not parallel. The later is the most common.
It is possible to make seams parallel in both directions by rubbing each part along a sheet of 240 or 150 grit laid on a perfectly flat surface. If your benchtop is not flat enough, set aside a foot square block of MDF.
There are many ways to sand or smooth the seam after gluing or applying filler. I rarely use sandpaper. I prefer filing or scraping. Very nice needle file sets are available that cut fast buy leave finer scratches than medium sandpaper. Only problem is that styrene dust is hard to clean out of files, and though soft can dull the files in time. I go through about two sets a year.
Scraping is very seldom discussed but is an excellent technique if you master the skill with a bit of practice. Scraping is a centuries old skill used in carpentry and machining to get a flat, smooth surface.
I do scraping with a hobby knife. I keep one handle with a blade just for scraping. It does dull the blade fast. And, I use a blunt point blade, not a sharp angled one like an 11. The blade is held at almost but not quite 90 degrees from surface, and about 90 to the direction of the seam. The top of the blade should lean very slightly towards the direction of movement, and you move the blade along the seam. It smooths well and with proper technique leaves no scratches in the surface, so no sanding is needed.
Try searching for "finish scraping."