As you've found, TG2 makes it very easy to create semi-random, procedural terrains with lots of detail and variety. Getting explicit forms is a bit more of a challenge. There are several possible approaches which I'll outline (but not yet detail) below.
The first point that should be made is that the best approach to terrain building depends somewhat heavily on your final goals, what you are going to do with the terrain. More specifically,
if you have little or no interest in
actually rendering a terrain with Terragen and you instead intend to import it into another program to render, or use it in a realtime game engine for example, then using TG as your terrain *builder* may not actually be the best approach to take. While TG2 is a very powerful and capable terrain generator, much of the benefits it has are confined to its procedural functions, the details of which simply cannot be exported to other applications at this time (imagine billions of polygons of terrain geometry being imported into Maya).
So, if the goal for your terrain is not a TG render (at least in part), consider a dedicated heightfield modeler like World Machine, Geocontrol, Leveller, L3DT, Wilbur, etc. This means you would basically skip TG, not use it at all. It may simply not be the right tool for your needs.
Now, even if you do intend to render in TG, using 3rd party terrain modelers can still be a very good option. They provide much more extensive tools, particularly in the area of heightfield-based modeling, erosion, and explicit feature editing and generation. For example Geocontrol has very powerful combined painting/spline and procedural functions to create semi-random terrain with specific shapes. World Machine has powerful spline support for creating e.g. a mountain range, driven by procedural noise functions for natural randomness. L3DT has similar functions. Leveller and Wilbur are even more "painting"-oriented, but you can run post filters to roughen things up and make it look more natural.
If you don't want to buy these programs, can't live with the limitations of their free versions (mostly limits on terrain size), or if Wilbur (free) is not capable enough for you, or perhaps you just don't want to learn yet another tool then...
Consider hand-painting a base terrain map (or mask) in an image editor like Photoshop. You simply paint with gray-scale values, 0-255 shades of dark-to-light, with dark being "low", light being "high". This can be trickier than a dedicated heightfield modeler as heights are relative to scale once imported into TG2, and it can be challenging to actually paint more subtle altitude variations, but if you're already comfortable with an image editor it can be a good way to lay down a base terrain. Once created, you would import into TG2 and use it to drive base displacement, upon which you could add additional displacement functions for random and realistic variation. Alternatively you could paint a mask to apply to the random procedural terrain, using black for "don't show here" and white for "show full effect of procedural terrain here", and everything in-between of course. I imagine you're familiar with these concepts given what you've described above, but for the sake of being sure, I've explained a bit here.

Ok, so how about working *in* TG2 to get what you want? Well, there are a couple of options, depending on just how specific you need your terrain forms to be.
You can use the built-in Painted Shader either as a mask (similar to the Photoshop painted mask) or to directly drive displacement. This is a good option for rough masking and base displacement forms, but can easily be over-used, and the Painted Shader does not currently handle large amounts of data (paint strokes) that efficiently.
Another approach, more complex still, and less explicit but still powerful, is to use function nodes and mathematics to create masks or drive displacement. This is probably the last approach I would recommend, but it's worth mentioning just as an option.
- Oshyan