I recommend checking out this tutorial:
[ame="http://www.orbithangar.com/searchid.php?ID=3403"]Tutorial: Concepts for Interplanetary MFD 4.2.1[/ame]
It's for an older version of IMFD, but it explains the different types of transfers in a way that's quite easy to understand. The theory it contains will be useful no matter what tools you decide to use.
I haven't gotten Jedidiah's new nav tool to work on my PC, so I can't say much about it other than that it looks promising. Aside from that, there are two main choices; IMFD and TransX. Both have their strengths and weaknesses.
TransX is quite capable, and for multi-sling trajectories it's the only real choice. It's main "weakness" is that you need to understand the mechanics of the transfer fairly well to use it. Flytandem is the undisputed master of TransX, and has produced quite a few high quality tutorials for it.
IMFD's main weakness is that it isn't capable of planning slingshots, but it CAN execute slings. You'll need to find a valid launch window some other way, and it helps to know the altitude you should have for the swing-by if you want good fuel efficiency.
For a trip from one planet to another, IMFD can be very simple to use. There is a simple, repeatable process that allows you to find launch windows and plan the trip - even if you don't understand the mechanics involved. As you gain knowledge, there are more advanced features you can use to optimize the transfer. It also has an "Autoburn" feature that will make the burns for you (or you can perform them manually using the "Burn Vector" view).
To learn IMFD, I recommend "IMFD Full Manual / Playbacks":
[ame="http://www.orbithangar.com/searchid.php?ID=4142"]IMFD Full Manual/Playbacks[/ame]
This contains a PDF that is a bit easier to understand and more complete than the manual that comes with IMFD, and contains several annotated flight recordings showing how to use the various "programs" contained in IMFD. IMFD is actually a collection of separate programs that are designed to work together, and can pass information between themselves. These programs are used in sequence to complete a flight. For instance, to get from KSC to Olympus base you would use Target Intercept to plan the transfer. Then Surface Launch is "connected" to Target Intercept, and provides the launch timing and heading that allows you launch into the proper plane. After that, Orbit Eject is used to fine tune the parking orbit's plane (if needed) and perform the transfer burn. After that, Target Intercept is used to perform MCC's. Once you get close to Mars, Base Approach is used to fine tune the approach so that your orbit will pass over Olympus base, OR, it can plan for a "direct re-entry". Finally, Orbit Insert is used to insert into a parking orbit (or not, if you use the direct re-entry).
IMFD's Map program is the most accurate trajectory predictor available for Orbiter - it offers fully multi-body predictions and accounts for precession, non-spherical gravity, etc. It can be used to show your actual trajectory, or a hypothetical trajectory generated by one of the course planning programs like Target Intercept.
There are a couple errors in the sections on Slingshots and Target Offsetting, but it will teach you the process I mentioned, and contains a wealth of useful information. Mark and I are working on an update that corrects those errors and adds some new techniques, but it's taking far longer than we would like. That's my fault - something always comes up and prevents me from finishing my end of this. I hope I can get it done in a few weeks - but I've been hoping that for a few months now so I hesitate to make any promises. I'll help out with IMFD as much as I can, but I don't have internet at home at the moment so it may be a few days before you get a response from me.
With IMFD, you may not understand what's going on at first, but if you pay attention during the flight you can figure it out after a few flights. Artlav's new trajectory display may be very handy at providing the situational awareness that will help with that.
