I switch the object filter to ALL, type in soulgem at the top and choose the soul gems with the purple 6 to the left of there names. Problem I have is when I load up skyrim, and try to interact with the Grand and Black soul gems, they have the red Steal indicator under the name? Why is this, none of the other gems have the same problem, and what does the purple six beside object name mean?

The '6' is just the type of object. that type being a 'Soul Gem'.

Open >Items >Soul Gem and you will see this.

If its 'stolen' then the cell its in, or the container its in belongs to an NPC. It aquires its ownership from these.

Good call, I'll try to edit the owniship info of the cell.

Also, how do i get items to stay exactly where i tell them to? the gems keep falling over when i load up.

You should not be loading with a dirty save game. Sounds like you are loading your game while in the cell which means you have possible garbage in your save game from previous incarnations of your mod.

You can also check the 'do not havoc settle' on the objects properties.

Thats exactly what i was doing wrong thanks again!