As an experimentalist, I might not be the person best suited to answer this, but I'll give it a try.
The wavefunction is going to be difficult to visualize because in general it is a complex function. If you want to 'see' sqrt(-1), I suggest you resort to drugs, lots and lots of drugs. But as for physical interpretation, <PERSON> tells us that the amplitude of the wavefunction squared will give you the real probability distribution. So the wavefunction represents a probability amplitude, and the random nature arises in the measurement process.
When making a BEC, you extract energy from the atoms in a few ways. Usually, you start with laser cooling (in a magneto-optical trap, or MOT) that captures and cools about 1e9 atoms to about 100 microkelvin. From there, you often need to employ other tricks to beat the so-called doppler limit set by the linewidth or your laser. Another limit is the "recoil limit" that says you will never cool an atom to have less energy than the photon it (randomly) emits. So you turn the lasers off, and trap these very cold atoms in other ways only to cool them further. Either magnetic fields, or far-off-resonance, focused lasers (optical traps) are used to capture the atoms, but now we are not scattering lots of light off them like we were in the MOT. In both cases you are altering the energy landscape experienced by the cloud, and this causes it to seek the lowest energy. Lower the trap walls, and the hottest (fastest) atoms will escape, leaving the remaining (slower) atoms to thermalize to a lower temperature. This is called evaporative cooling. In magnetic traps, it is often done with radio frequencies which couple your atoms to different <PERSON> sublevels, changing their potential energy, and ejecting them from the scene. In far detuned optical traps, they just lower the laser power.
As the atoms get colder, something remarkable happens. Their wave nature starts to emerge. The de Broglie wavelength gets longer as you get colder, until eventually, particle wavefunctions start overlapping with their neighbors. At this point, the atomic statistics are no longer well described by the good-ole Maxwell-Boltzmann distro, and we have to resort to Bose-Einstein statistics. (This of course assumes you are working with bosons, or integer spin particles.) What does that mean? Basically it means that particles start to favor occupying the same state, or 'mode'.
To determine the wavefunction of a BEC, you could start with the <PERSON> equation, where now you simply replace the single particle wave function with a many particle wavefunction that is built as a tensor product of the individual particles. 580
This turns out to be a poor approach because the particles interact. They are constantly bumping into each other, and this manifests as a non-linear (i.e. density dependent) interaction term in the Hamiltonian. So we can far better approximate the situation with the Gross-Pitaevskii equation. If you want to model a BEC, the GPE might be a good place to start.
One of the striking features of QM in my mind is that the description of a particle is inextricably linked to its environment. It's right there in the GPE via the potential energy term, V. The solutions of this equation will be your wavefunction. When you confine atoms in a harmonic trap, one that looks like a parabola, your wavefunction will reflect this. Indeed it is not a gaussian you see, but an inverted parabola (see Thomas-Fermi approx.). It will look different in different traps. The residual gaussian is composed of thermal atoms, still described by the M-B picture.
I should note that when atoms are in the ground state, they still cannot be said to have "no motion". The uncertainty principle tells us that they will always smear out over some tiny volume of phase space. This is called the zero point motion.
The phase is a tricky subject. You are right that the book seems to have described it poorly. BECs are often said to be phase coherent, which is to say across the whole cloud, the phase will be the same. If it were not so, you would necessarily see striations since some of the atoms would destructively interfere with their neighbors. This is basically an excitation, and so energetically unfavorable. I might have just made a theorist lose her lunch with that explanation, but this whole thing is just meant to be a low level intro.
Good luck, and keep asking questions. 795