Spricigo

A bit overkill ( RA-15 should be strong enough), but OK. I hope you remembered to phase then 180° apart so at the time one is at PE the other is at AP.
Ok, and what you will be using in the later ships? You need to consider that before deciding in how high the relays will orbit. e.g.
A)Your ships will have just a communotron 16 each (VAP 500k), so the range will be: SQRT[500k*2G]=1Mm You need the relay well bellow Ike's orbit to ensure connection in Duna's surface/low orbit
B)Ships will have a DTS-M1 (VAP 2G), the range will be comfortable 2Gm The relay can be anywhere within the SoI , only LoS issues will prevent the connection.
Considering the above my suggestion is definitely below Ike's orbit. Anywhere between 320km (lower Duna may block the signal) to 1Mm (so you don't need stronger antennas than Communotron 16 on the other ships). Notice:
1.Range between you polar and equatorial relays is 14Gm
2.Range between polar satellites and Communotron 16 is 7Gm
3.You may still have LoS issues while behind Ike.
 
About Ike: if you are worried about losing signal behind Ike, HG-5s in triangular formation between 130km and 1600km close the gap nicely. 
 

seems like a problem since in the mod thread the developer ofer only two download links: spacedock and curse . He even have a video explaining the process and mention than you can also get in on CKAN.
Follow the instruction on the video, if you still can't get it to work maybe ask in the mod thread.
And for your own good, don't click on download links that you are not sure is what you are looking for.

I was under the assumption that one cannot use RCS under limited control.
@BjM Duna will be around 3Gm away from kerbin at closest approach, for the sake of analysis lets suppose it will not much farther away at the time of your mission. Lets see your options:
1.Going for a kerbaled mission with a pilot will give you full control of the craft regardless of commnet coverage, the drawback is the added mass to support the crew. A orbit Duna and return mission requires less deltaV (but a bit more precision) than Land on Mun and return.  In any case you should consider bringing more fuel so you can explore a bit, visit Ike and so on.
2.Upgrading the tracking station to lv3 and piling up15x HG-5 will provide a max range over 3Gm 20x will give 3,43Gm.
3.Unlocking the DTS-M1 (or RA-2, in the same tech node) will allow a range of 10Gm between the craft and a lvl2 craft station. Requires 160 science and unlock a few other parts (personally I find the HECS probecore  and the TR-2V decoupler very handy)
4.Just send the craft, you don't need commnet control for a flyby, and if Duna don’t disturb the trajectory too much the craft will eventually come back near Kerbin to transmit the science. If you set a maneuver node and point the craft in the required direction with antecedence you will have no problem following it even with limited control.

http://wiki.kerbalspaceprogram.com/wiki/CommNet
The important bit:
Range = SQRT ( Antenna Strength 1 * Antenna Strength 2 ) in case a Commonutron 16 talking to a HG-5:
Range = SQRT ( 500k * 5M ) =1.58M  
Oops!

http://wiki.kerbalspaceprogram.com/wiki/TR-18D_Stack_Separator
 

All you need is three satellite in a roughly equatorial triangle formation to cover everything except,  maybe, the poles.  If MJ don't have a routine for this at least the readout of orbital period make it trivial. 
There is a example of how it's done : 
 

Notice it depends on how you make the trip. If such small details as "deltaV budget", "cost", "complexity are not a concern you can do it much faster with a brachistochrone trajectory.
https://alexmoon.github.io/ksp/ helps.
After plotting a transfer the selected result details show, among other things, transfer time
Open advanced setting to set a lastest  departure time and maximun tranfer time.

Not in stock. There is a few mod option if you want to circumvent the whole clicking for science altogether. Examples:
 

Lets do the math and find out.
VAP = Stronger AP * ( Sum of AP / Strongest AP ) ^ ( Average Weighted Combinability Exponent for Vessel )
Range = SQRT ( VAP1 * VAP2)
where VAP =Vessel antenna Power, AP=antenna power, Combinability expoent its 3/4 for all antennas except Communutron 16 and 16S (we'll use 3/4 for this case)
RA-2, rated at 2G; RA-15, rated at 15G; RA-100, rated at 100G
For 1x RA-2 to 1xRA-2  range = 2Gm
For 1xRA-100 to 1xRA-2 range=SQRT(100*2)=14,14Gm
For 2xRA-2 to 2xRA-2 VAP=2*(4/2)^(3/4)=3,36  range=3,36Gm
For 1xRA100 to 2xRA-2 range =SQRT(100*3,36)=18,33Gm
For 1xRA15 to 1xRA-15 range=15Gm
For 1x100G to 1xRA15 range=SQRT(100*15)=38.73Gm
Jool SOI radius 2,5Gm
Pol Semi-major axis 180Mm
 
 

@NecroBones Explain it way better than I may dream to do.  Hope it helps you. (definitely helped me)