@Stevie yup the trees are just tiled and when you import them you can only use one texture, but there is a very simple work around for this.
I'll use the demotree1 for this example.
First have your tree fully ready to export how you would like to see it in the game. The only thing i did was move the lower stump out some and make the tree a bit thicker.
Go to leaves in the tool bar and remove all leaves, this will leave you with the trunk and the branchs. Export this as your trunk.x model that will be used for the tree.
Next go back to your leaves in the tool bar and open leaf menu. Generate branch leaves, and you sould be right back to the same tree you started with. Then go to trunk operations and reduce the trunk settings, tapertrunk, Upper stump, Lower stump to 0 then reduce the thickness to 0. I say this order cause sometimes treemagik will send the leaves and branchs off to the side if you reduce in another order or reduce the model to fast. If this happens just resize up your thickness and your branchs and leaves will be brought back to there orginal position and reduce the thickness again usually however sometimes your model gets lost. Last click branchs remove all branchs, and you should have just your leaves, with very thin small line for a trunk under them.
Export this as leaves.x so now you will have 2 .x models, and your textures (of course you have to convert these to tga, or .dds) 1 model for your trunk and branchs, and another one for your leaves. Just put these models in like you would any other fpscreator entity and in your .fpe for these models just point each one to its own texture file. In fpscreator the alpha does not show up in your editor so you trees will look like a mess showing the full leave polys and you will see the small trunk poly under the leaves.
Just line that line up with center of your trunk model and test it. And the tree will be in fpscreator.
At first it seemed like it was a pain to get them in and that i would have to remap them all but its actually quite easy and much faster then uv mapping out a tree's, at least for me it is. And i didn't want the money i spent on treemagik to go to waste.