Greg,
That sounds like it's the Marias Pass or Montana Rail Link layout, yes? (Kalispell is in northwestern Montana just west of Glacier National Park, excellent town, spectacularly beautiful country, probably the westernmost Hardee's

, sorry if you knew all that)
Unfortunately that session isn't in my UK version of TRS2006 so I can't check it. (Other guyz, is it in the US edition, or TRS2007 perhaps?)
stop when the consist clears the junction
Your train needs to stop far enough away from the junction to allow the junction to change direction, presumably so you can then go in the opposite direction down the other track. Allow maybe two or three loco lengths from the junction but it can vary. You almost certainly need to come to a complete stop, not a crawl. If it's on a gradient then you might need to apply some power in the opposite direction or apply the brakes and this will vary between DCC mode and CAB mode. DCC is simpler, CAB is more realistic. (Applying opposite power to keep stationary is a total no-no with real locos with electric-powered wheels as it will burn out the electric motors but ok in Trainz)
For a glossary of terms relating to real railways, Trainz and computers, try
this.
And how do i know if this is the demo version or not? I bought it a while ago but don't remember where? How do i get the full version is that is the case. I am not into building and all that i just like ot drive and transfer cars in the rail yards.
It is a demo. There are various full versions and their relative merits are hotly debated here. I'm going to go out on a limb and advise TRS2004 (should be budget software now) or not quite so good TRS2006 (also budget), then register with us (Razorback Railway) to give you access to a wide range of activities in which you do the driving. OK shameless self promotion over, now the other guyz can say what they'd advise
This level of confusion is totally normal when starting out with Trainz. Things will become clearer and much more enjoyable as you spend more time with the program.
HTH, John