Should I isolate the freight and the passenger?
Maybe create a second track parallel so that they don't use the same track?
In my personal opinion, yes, add the track so that they can work independently. This is how it would work in the real world - no freight company wants some passenger train holding up a few thousand tons worth of products. That's a pretty expensive hold up.
However, this is a model and you may choose to otherwise. How would you want to operate the layout? That's really what it comes down to.
Here are some questions which I need answers to:
1) I need rail joiners for Atlas 100 and my hobby shop supplier (1 hr drive away) is out of stock now for 1 month. Any suggestion on where I can order some?
2) Since my train knowledge is very limited, do I need a locomotive for every yard? (I would need 5?)
3) I have Atlas flex track, I was told to use Peco turnouts, is this right and do I need special joiners since 2 different companies?
4) Are the turnouts all manually triggered or are there any that can be electronically controlled?
That's it for now
Thanks
1. I get most of my stuff from here:
http://www.modeltrainstuff.com/ However, there are a few sources around the web, some better than others. Surf the forum for these resources, there's quite a few good ones. Beware: shop around on the web the same you would for anything else. Some shops have better prices than others.
2. Die hards will put a locomotive in each yard. I personally don't have the money to go buy 5 locomotives, even if they're just small switchers. If you have one or two right now, use those. As time goes on, you can decide if you want more.
3. This is exactly the setup I have. The only issue is the height of the ties. The PECO ties stand taller than the Atlas ties. The rails are same height (code 100 is code 100). Because of the ties, the rails end up at different heights. I ended up putting shims under the Atlas track just before/after the PECO turnouts to resolve the issue. A little bit of extra filing on the top of the rails after soldered together will also help smooth the transition.
4. They can all be electronically controlled. Tortoise machines are typically the weapon of choice. They mount under the table and are pretty reliable. With the mounting style, you can put ground throws on the surface that will turn with the track. It's a pretty cool result. The nicest ground throws (in my opinion and many others') can be found here:
http://www.cabooseind.com/
I hope this answers your questions.