Congratulations on trying something diffirent, I built that model when I was younger.
The holes on the sides are limber holes.
You should find everything you need detail wise over on the AMP forum, look for Siara's build which can also be found on the SubSim forum, keep in mind his build is an extreme example being done with the Revell 1/72 but it still has tons of good info.
Addition resources can be found at U-Boat Archive, ubootwaffe. U-Boat, also google search U-99, U-Boats, U-Boots, German Submarines, etc... many of these will five you othe model builders examples on what they did or are currently working on.
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