Take pride in your work here
This is an area where your individuality, care and precision can really make a difference in performance and serviceability. When I originally put the inlet flow smoothing panels inplace I did not close in the sides. After quite a bit of flying I went back and closed in the sides (all four) with blue foam and sealed over them with fiberglass (I use EZ-Poxy brand from Aircraft Spruce). In shaping the foam I cut it back under as it approached the cowl surface before the fiberglass operation so the baffle seal would be allowed to lay flat against the upper cowl in this area as it did before the plugs were added. I did this as a speed mod thinking that air tumbling off the edge of these "ramps" curling back on the underside had to create drag. My flight test revealed no change in speed as a result of this mod so I left it. When you install the upper cowl with the ramps plugged be sure to stick you hand in the inlets and guide the rubber seals into proper position (not binding with gaps in the seal).
I tried extensive baffling in the lower cowl and came up with a configuration that gave a 4 kt increase but most of the changes actually slowed the plane down. My point is, this is an important part of building the airplane for engine health and airplane performance and you should focus on creating the best installation possible instead of letting it drive you to anxiety.
Bob Axsom