I think you've confused yourself a little bit.
Hohmann Transfers do
not have constant velocity during the transfer. As the object goes outward from the gravitating body, it loses velocity, just the same as you lose upwards velocity when you jump.
What remains constant is the total
Energy. The spacecraft loses velocity (which can also be counted as Kinetic Energy), but it gains Potential Gravitational Energy. The two different types of energy flip back and forth as the satellite proceeds on its orbit, but the sum of the two remains constant.
Doing a thruster burn changes the energy of the system, because it converts chemical or electrical potential energy into Kinetic. Unless the orbit is circular, there is no time that the velocity needs to stay constant.
For ion thrusters and other similar types of propulsion, the equations become
much more complicated. To give you an idea, in my space propulsions class which is a 4th year class in an aerospace engineering major they only said _how_ it's done... we didn't have to actually do it.
Basically, you know the starting position and velocity of the spacecraft , and you consider the thrust, mass, direction of burn, etc. If you take a small enough time step, you then can know where the spacecraft is at the initital time + the time step.
The basic procedure is nothing more than
Euler's Method for numerical solutions.
When you couple this with a multivariable controller, you can get a grip on the maximum error you can expect to see over long durations. If that error is less than the mission envelope says it can be (for example you want the spacecraft to arrive at a planet at a certain time + or - 2 minutes) the spacecraft can get where it's going.
There are several software packages which are used to do calculations like this. One of them is
http://www.stk.com/ or Satellite Toolkit.
Hope that helps. Welcome to PF!