I'm not a big expert with TransX, and you haven't quite told me what I need to know. Sadly, I'm quite busy these days and don't know when I'll be online again so I'll try some generic tips and hope it helps.
It depends on what you mean by "integrate". Are you trying to follow a specific plan from TransX, or just using TransX to find a valid window?
If it's the later, you would set up a transfer from Earth to Jupiter in Target Intercept using the TEj and TIn shown in TransX (forget what TransX calls those - the TIn is probably the PeT at Jupiter, etc). Then use Planet Approach to try and tune the Jupiter periapsis and inclination when you are still about 3 "SOI's" away from Jupiter. Once you enter Jupiter's SOI, change Target Intercept to source = Jupiter, tgt = Saturn. Get your Jupiter PeT from IMFD's Map and use it for the TEj. For the TIn you can use the data from TransX, or just adjust it to get the lowest total dV as shown in IMFD's Slingshot program (set to course).
To more closely follow TransXs plan, you use IMFDs Delta-V program to perform the individual burns called for by TransX. Be sure that Delta-V is set to "Vel frame"< NOT "Apollo P-30" mode.
You need AT LEAST 3 seconds before TEj when you press the AB, but it's best to have at least 120 seconds to give the vessel time to orient itself. Usually, you can program the burns much more in advance.
In Velocity Frame mode, you have dVf (f = forward, positive values are prograde, negative values are retrograde), dVp (p = planar, positive values are Normal, negative values are Anti-Normal, is at right angle to prograde vector), and dVi (i = inward, is at right angle to the prograde vector, positive values are towards the reference body, negaitve values are away from it.
You will have to transfer the values from TransX, use the "Set" button to manually enter the number. The ++ and -- keys increment by 0.1 m/s, but greater precision is possible using the set button and typing in the number.
If you aren't familiar with IMFD's Map, the best settings for an approach is to have (for example) TGT = "jupiter", Cnt = "p-jupiter", then enable Int. You can see the results of a planned burn by enabling the "Plan" button. Trajectories shown in green are actual, shown in blue are hypothetical.