The clips are supposed to go between the pillars – so there’s slots for three clips side-by-side if you fill them all. You should usually only need one clip in the center gap. Pop the clips in the right spots and you’ll be good to go! =)
I had a similar problem with my Elven Sky Reaver. I got a tube of inexpensive wood putty. I glued the parts together then worked the putty into the gaps, used my fingers to smooth it out, then used a knife once it cured to shape the surface a touch more. I like wood putty with 3d printed models because it’s formulated to not shrink as it cures so you get a nice consistent finish. It’s also sandable, primable, and paintable.