How can I dock two ships already in orbit

[LABHOUSE]

I used the same rocket to launch each one the target ship has some fuel left in the rocket because i have not decoupled yet and the other rocket has the same amount of fuel and the payload has some fuel left.

[TopGull]

First, make sure you have a docking port and RCS thrusters on each vessel (if not, redesign and relaunch), then go watch Scott Manley's orbital rendezvous tutorial on YouTube. He does a great job of explaining the maneuvers.

[Pecan]

Check the tutorials listed in http://forum.kerbalspaceprogram.com/threads/28352-The-Drawing-Board-A-library-of-tutorials-and-other-useful-information.

Broadly:

• Circularise the target vehicle's orbit as much as possible (makes it easier to get an intercept later), then switch to the docking ship.
  
• Establish a phasing orbit at a higher or lower alitude (this is so the two ships have different orbital periods and the lower one will eventually 'catch up' with the higher)
  
• Match planes (orbital inclination) with the target
  
• Create a manoeuvre node to raise your apoapsis (or lower your periapsis) to the target's altitude (but don't execute the burn yet!)
  
• Drag the node around your orbit and/or increase the orbit number (+ button) until you get an intercept as close as possible to the target (within a couple of kilometres)
  
• Make the burn
  
• Circularise at the new apoapsis/periapsis
  
• Switch to RCS and make short, low-power manoeuvres to approach, align and dock with the target (keeping the relative velocity low and docking at ~0.1m/s)
  

[cantab]

Here's what I'd do:

No need to change the target ship's orbit. Set it as target when you're flying the rendezvousing ship.

The following assumes rendezvous with a ship in a higher orbit. Change appropriately if the target is in a lower orbit.

Set up a prograde burn that raises your apoapsis to just touch the target ship's orbit. Put this manouevre:

if you have a big inclination difference, at the AN or DN, whichever is closer to the primary (Kerbin for you).

if the target orbit is very eccentric (yours isn't), directly opposite its apoapsis.

otherwise, at your periapsis.

If your inclination is more than a degree or so different to the target, set up a normal burn at the AN or DN, whichever is further from the primary if there's a big difference. You may need to add a retrograde component to keep the apoapsis in the same place. You should after doing this, if you didn't already, have a closest approach marker. If the AN/DN is at apoapsis, combine this burn with the next one.

Set up a prograde burn at apoapsis that gives you a closest approach on a future orbit as small as you can get. For typical rendezvous in Kerbin 2 km or less is what you want. Optionally, add further dummy manouvres around the orbit, each one just before the last (because actually that places it nearly a complete orbit after), to show the closest approach for more orbits in the future.

Once you have that set, set the navball into target mode by clicking the speed indicator. This measures the prograde and retrograde directions and speeds relative to the target ship rather than the planet. When you get close to the target, point retrograde and burn until the speed shows zero. Congratulations, you've rendezvoused! Now carefully fly closer to dock or just EVA Kerbals over.

[LABHOUSE]

Well the target ship is not up to date so I shouldn't even try to dock because I won't be able to land it on duna (I'm docking a ship to it).

I will launch another target ship.

[Wanderfound]

Well the target ship is not up to date so I shouldn't even try to dock because I won't be able to land it on duna (I'm docking a ship to it).

I will launch another target ship.

You'll find it a lot easier if you first build and launch a pair of small, manoeuvrable ships with docking ports and practice rendezvous and docking with them (which is what NASA did). It's simple once you've got the knack, but when you're first starting out doing it with large craft is painful.