Using the scenario you provided as a starting point:
First, open Orbit MFD on the left side, set the reference to Mars, target Phobos and select the equatorial frame. You'll also need to switch the distance to altitude. Make a mental (or physical) note of Phobos' inclination and average orbital altitude [(PeA+ApA)/2]. While you are at it, also press the HUD button to view your orientation relative to Mars on the hud.
On the other side, select IMFD→Course→Planet Approach and set the reference to Mars.
On the side you had Orbit MFD, Open IMFD, connect it to the IMFD on the other side and open the Map program. Set the reference to Mars and target "l" (letter l for equatoria'l').
Enter Phobos' inclination on the Planet Approach program and the altitude you want to perform the aerocapture. With this periapsis velocity, I'd go for ~25km. Notice that the EqI value on the Planet approach program cannot go below a certain value.That's because the starting point of the scenario is too close to the periapsis arrival. Doesn't matter though, it will just cost a few m/s of dv more to fix it.
On the Map side, press Plan to view the result of the maneuver. The blue dashed line that ends with a small box is the line of nodes relative to Mar's equator. (you targeted "l" remember?). That's where the plane of your trajectory (after the maneuver) and the equatorial plane of Mars intersect.
On the side with the Planet approach program, adjust the EqI and PeA values, until the periapsis altitude on the
Map program is where you want it (~25k) and the line of nodes passes exactly over the periapsis.
Now that you know exactly what the result of the burn will be, go ahead and autoburn the Planet Approach program.
Remove the "Plan" from the Map, so that you can see the actual trajectory. Notice that so far, we haven't target Phobos in IMFD.
After the burn is completed (cost ~80 m/s), coast until you are near the Martian atmosphere (alt ~150k) and open Align Planes MFD→Target Phobos.
On the other side open Surface MFD. Also switch the hud to Surface mode and press Ctrl-/ to switch off the attitude RCS. (No need to waste fuel, the atmosphere and the dynamic surfaces of the Deltaglider are enough to help you orient the spacecraft).
Once you are deep inside the atmosphere that you can control the bank of the spacecraft, full trim up and bank to the side that gives you a negative rate in the Align Planes MFD, so that the RInc is getting smaller. You need to watch 4 things. Vertical vel and vertical acceleration on one side, RInc and Rate on the other.
Your goal is to get the RInc as close as you can to 0° on Align planes MFD and to get the vertical acceleration to ~0 when the vertical velocity is close to 0.
Once you get the Rinc as close to 0 as you can, bank inverted and focus on keeping the vertical velocity close to 0 by adjusting the trim.
Switch the side with AlignPlanes MFD to OrbitMFD and keep an eye on the eccenticity. Remind yourself of Phobos' average orbital altitude (~6M meters).
Wait until you get captured (ecc < 1) and switch the side with Orbit MFD to Aerobrake MFD. You will find a very useful value there; the Apo Alt. This tells you what your apoapsis altitude will be after the aerocapture. If you don't see that value, it means that you are going to hit the planet's surface. No need to worry though; just adjust your trim until you see it.
Bank the spacecraft upright (in one quick smooth motion, so that you don't mess up your RInc to Phobos) and adjust your trim while looking at the Apo Alt value in Aerobrake MFD. You want to get it to ~6M. If neccessary, also pitch up or down the spacecraft a little bit.
Stay on top of the Apo Alt value, keeping it close to 6 - 6.1 M, until you are on your way out of the Martian atmosphere.
Time to set up the intercept to Phobos. Use IMFD's Course→Target Intercept program and target Phobos. Adjust the Tej, Tin values until you have a minimum Total dV. Once you have it, go ahead and AutoBurn it.
After the burn is completed it's good to have TransX targeting Phobos on the other side, . This way you'll be able to see the closest approach to Phobos, something that IMFD's map program can't do. This way, instead of setting up MCCs, you can easily use a little bit of linear RCS to fix your approach to Phobos if it strays too far. You'll probably need to do this once or twice, depending on whether you are flying with non-spherical gravity turned on or off. Or you can re-adjust the TIn in IMFD's Course program until you get a new minimum dV solution and AB than one; whichever suits you best.
After the MCC, all that remains is to match your velocity to Phobos. You already know the dV you'll need from the Target Intercept program (iV on the bottom left) but at which distance from Phobos do you need to start the burn? you can use IMFD to find out.
Wait until you are close to Phobos (alt ~200km on the hud) and open Orbital→Match Velocity program. Target Phobos.
Multiply the burn-time with the dV and divide by two. This will give you a very good approximation at which distance from Phobos' surface to begin the burn.
In this example the dV is 674 and the BT is 35.28. 674x35.28/2 = 11889.36 meters. Round it up to 12k. Orient the spacecraft to get the cross in IMFD's Vel match program centered and repeat the calculation when you are closer (~50 km).
674.5x35.3/2 = 11904.925, round it to 12k. Very IMPORTANT: That's the ALTITUDE when you'll begin the burn, NOT the distance shown in IMFD,
All done, go ahead and land it.
Delta-V used:
--------------------------------------------
80 m/s (Pic 3 Planet approach)
8.0 m/s (Pic11 Target Intercept)
~5 m/s MCC
675 m/s Phobos velocity match
Total: 768 m/s.
USE TRANS.......oh 
