I avoid the invisible signals as they are completely unnecessary if you are using Jointed Rail's scripted signals.
The spacing between signals is determined by the following factors:
Train length
Train Speed
and
Train frequency
If you are running mile long freights at 40 mph max speed you can place your type 05s a mile apart and probably never see a yellow, if you only run a train every hour. If it's a commuter line running frequent short consists at a higher speed, you want closer signals so the trains can run behind each other.
If any of your junctions are not set for the mainline, you will get a yellow. With multiple Type 05s, you will get a blinking yellow followed by a solid yellow before the red. This is standard for NORAC operations. The blinking yellow is to tell the driver that there's an upcoming yellow and to start slowing down before the solid yellow. A solid yellow will tell the driver to operate at one half the posted speed and to prepare to stop at the upcoming red.
Crossovers... If you use Type 08, interlocking signals, your trains will operate at a slower speed through the interlocking. I think they drop down to 15 or 20 mph. I can't remember since I haven't done any driving for ages, or even used Trainz in months for that matter. Again if you are using JR's scripted signals, you can set the mainline path and I think that will keep the trains at speed.
How do I determine signal spacing?
I setup a double US Coal 2000T consist and use that as a spacing tool. My Type 05's are placed at the "forward" end of the consist as I move it along the tracks with a bit of a fudge space if here's a crossover or single to passing siding where in these cases, I end the Type 05s shorter long before the upcoming Type 08s, or Type 04/Type 06 combination.
Hope this helps.