right - first thing first.
You NEED to go to the simplify3d website and WATCH ALL THE INSTRUCTIONAL VIDEOS ON HOW TO USE SIMPLIFY3D.
That's the first thing :-)

Second.
you clearly have more on the build plate than just the bit you showed in the pictures.

When you click on any one of the seperated parts, it will select that part and it will show up as selected on the plate.

So you can remove or move the selected bit and ignore or remove the others.

But if you went and spent a couple of hours learning how to use s3d it would improve your life immeasurably :-)

same goes for flashprint - I can show you what to use, but unless you want to give me some money, I can't/won't do it for you.
:-)

ie: I can use rempre support software to do it for you and give you some tuition - but not for free :-)