Sadly the maneuver planner isn't really suited for that kind of accelerate halfway, then decelerate transfers. Even though it calculates burn time, it assumes in the orbit calculations that the change in velocity is instant. And it won't work while docked, because it needs a current orbit for that.

You could try about halving your deltaV (accessible in the F2 infoview screen), enter that much in the planner, but it will be quite finicky (I just tried).
You also can advance and rewind time in the orbit map to check orbits, you don't need to time accelerate for that.
The flight UI will then tell you the burn time, but you constantly need to cross-reference with that, but since our ships are so strong, at a longer trip you hit half of your deltaV much sooner than the half-point of your distance. For that reason, and because the ships aren't constant acceleration, because of the changing mass while you burn your fuel, the brachistocronne equation will only give a rough estimate of travel time as well.
(yet, I'm working on a rebalance that mostly fixes accelerations, exactly because it easier to fly that way, and to avoit overly strong final acceleration values, like 20ish Gs).

But: we do have an UI for these kinds of transfers in the flight HUD. It won't give you the travel time, but will tell you when you need to flip and start decelerating, and also shows your deltaV against your current speed, so you won't run out of fuel.

Thank you very much nozmajner for your response and details. I have read the link before posting and figured out that you need to be in the 'Coasting' phase for these 5 tabs to make any sense, despite of that I was never able to plan a maneuver with them, but the flying UI in the Front View gives all details about *when* to turn your ship arround, but it would be very fine to have an anticipated ETA like for these formulas (see below).

Very long ago I have made a personal help file for Frontier Elite II as for planing ETAs on long travels in order to know wether I can accept delivery missions after hyperdriving. Here the excerb:

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1. ETA CALCULATION (Estimated Arrival Time)

For most missions it’s important to accomplish them in time and therefore it’s crucial to know when one could expect to a) arrive in a system and b) to know the necessary time to travel within the system to a destination.  With a constant acceleration and using the main engines to decelerate, here are the precise equations:

v_tp = sqrt(a d);     t = 2 sqrt(d/a);    

v_tp     =  velocity at turning point d/2 in meters/second

a          = acceleration      9,81g x ship main engine acceleration (in g)       

d          =  total distance  in meters           

t           =  time for destination  in seconds

The formulas above provide precise calculations, but in practice one should calculate unpredictable events, like attacks and flight path deviations designed to avoid attacks etc.

The lists below give MINIMUM SAFE VALUES which are not 100% accurate, but include such unpredictable “time losses”, adding a 15% tolerance and cutting the result to a higher value.

As every ship has different acceleration capabilities, be sure to refer to the correct ship.

EAGLE MK I (a=25.2g) 247,212

2. GENERAL NAVIGATION PROCEDURE

The general procedure is: look at the distance to travel and remeber HALF that distance. Accelerate until arrived at half the distance, then make your ship a 180° turn and set the speed to 0. You should come to a halt a bit before your destination.

Within a body’s orbit, I recommend a speed of 30 km/s and a descent speed of 20000 km/h. This descent speed gives you enough time to brake (pointing towards the sky) as soon as you get an altitude reading (from 60000 m downwards).

2. FUEL CONSUMPTION

The Hyperdrive fuel consumption is: (hyperdrive class)^2 = tons of fuel for maximum drive range in 7 days.

For less than the maximum drive range, the consumption and the time are linearly less.

Within a system, 1 ton of fuel is sufficient for 50-70 AU.

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The numbers for the hyperdrive classes and fuel consumption are of course different now in Pioneer, also the introduction of 'Delta v' makes Coasting much more frequent and the formulas need to be adapted.

Yeah, such a table might not work as is. I was thinking about doing something similar to that, but my limited math knowledge provided a nice brick wall I might want to try to surmount again sometimes.

On the other hand I did a bunch of thinking about such planner tool for the orbit map a while ago, and it would sure be nice to have one for such transfers. You setting up a route, even with multiple burns and such, and the autopliot would execute it. But note that this is just an idea of an artist who dabbles in the design and thinks about the UI, coding it is where the meat of the work would lie.