They look fine - you might need to adjust as you ride and see how the positioning feels.
The threaded parts (dark/black in your photo), I believe, are simply spare parts to use as needed. They are the threaded inserts that one would put inside the shoe, under the insole, if needed.
Since you were able to install your cleats, your shoes already have them. Sometimess those threaded inserts strip out and you might need to replace them.
I believe the other parts (silver) are also spare parts to use if needed. If you'd needed to use the threaded inserts, you'd use the silver parts to function as metal washers to support the threaded inserts, if you can follow me. They are slotted so that the threaded inserts can slide lengthwise along the shoe for cleat adjustment.
Just FYI - the threaded inserts inside your shoes are found by:
1 - removing insole
2 - look on the inner sole of the shoe and you'll either see the threaded inserts, or you will see a perforation in the material of the inner/bottom sole of the shoe. If you remove the perforated section, you'll have access to the bolts for replacement as needed.
Often / usually cleats come with printed instructions that spell this out, but it's pretty easy to figure out too.