Ordinarily this is what happens; the fixture is placed, the gum is
sutured over.  Sometimes the head of the implant fixture becomes
exposed; I've seen this happen, and while it isn't considered ideal I've
seen these cases work out just fine.
    The OP states that his implant is covered by a "manhole cover" which I
take to mean a healing cap.  This is done after second stage surgery.
After a few weeks the implant is ready to be restored.  But I wouldn't
attempt to cover an infected implant, and after all the implant is there
to use.  The rationale behind suturing over the fixture after placement
is that it gets to heal (osseointegrate) in a sterile environment, not
exposed to saliva.
    When implants fail to integrate, it is often not possible to tell why.
 One patient of mine had several implants fail; they were placed before
the risks of bisphosphonate use with regard to bone healing in the mouth
were well-known.  She did NOT suffer osteonecrosis; OTOH, the implants
failed, and the surgeons are considering the possibility that her
medications were related to the failure.  No way to know though, and
subsequent implants worked out fine.

Steve