G'day theedge2k,
I am sure I am not alone here in failing to understand why you are unable to get the Fishlipsatwork route you have downloaded to work in Trainz (they are designed for ALL versions of Trainz up to and including TS 2009, though it may be a little more difficult to get them into this latter version) - getting them into TRS 2006 should be a "doddle"!! Firstly, what source did you use to download the Fishlipsatwork file? As we speak, I am downloading the "New Jersey" from the Download Station using Download Helper. As far as I am concerned, this WILL proceed according to any other download from this location (a direct install into Trainz - in my case TRS 2004). The route will then be where it should be when I next open Trainz (though I should have perhaps, chosen a smaller route, the download still has 30 minutes to finish - I really must renew my FCT). If you went to fishlipsatwork's own site to download the file, then they are *.cdp files there too. Although you do not have the luxury of the Download Helper, it should be just a matter of going through the normal process of installing an outside *.cdp to get it into Trainz (knowing nothing about TRS 2006, I can offer no advice in this area).
As noted in other posts above, the only major hassle you can have with any of fishlipsatwork's terrains is that the TIGER liners do not show up when the route is installed. This can be overcome by installing the HOG textures (which you say you have done and which can be checked by looking through the available textures in your 'Paint Tab' in Surveyor). Once installed, the textures show up as a separate group under "HOG" (and can actually be applied to any terrain as normal ground textures).
If you have done all of the above correctly, there is absolutely no reason why the terrain (or the actual route, for that matter) does not show in Trainz. We are all at a loss as to your failure in this regard...
Jerker {

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P. S..
After the download was completed, opening Trainz revealed the new route to be properly installed with all the TIGER lines displayed in all their glory - the whole process should be no more difficult than that.)...
Jerker {

}