I have a small (three inch) Juniperus. I love the art of Bonsai and
patiently looking forward to my little tree growing. I have it in a small
plastic pot, should I leave it there for a couple of weeks or transplant it to
a Bonsai pot?

Sorry, but with bonsai, patiently is measured in years, not weeks. You can't
really do anything with a three-inch juniper, until you are very experienced.
Where do you live? If you are in a warm climate, put the juniper outdoors at
once and leave it there all year round. It is not an indoor tree. It needs to
be kept cold in the winter. If you are in a cold climate, wrap your tree in
plastic and put it in the refrigerator until March. Then plant it outdoors in a
growing bed until it is several years old. It may be ready for a bonsai pot a
few years later.
Iris,
Central NY, Zone 5a, Sunset Zone 40
"If we see light at the end of the tunnel, It's the light of the oncoming
train."
Robert Lowell (1917-1977)