I have just bought a 2014 mk3 1.6 tdi. I had the same problem with poor heater and discoloured coolant in the expansion tank. i tried the heater flap reset but this did not cure the problem. After trawling this forum it looked like the heater matrix was the fault. i checked the coolant pipes at the bulkhead as they go through into the heater matrix and they were just better than luke warm.
I did a ring round of the usual suppliers and the best i could get a matrix for was £90 inc vat. I'm in the trade so this was with trade discount. buycarparts.co.uk kept popping up on my browser so i thought i would take a look. The company is based in Germany but their prices are much much cheaper than anyone else. So i typed my reg number in and was given something like 15 options of manufacturer of a heater matrix that would fit my car. I opted for the cheapest one £20.99 inc vat plus delivery of £8.50 3-5 working days. it was manufactured by VAN WEZEL based in Belgium (checked their website).
Part came 4 days later unboxed it and all looked ok. drained the coolant from the car and removed and binned the mit silikat expansion bottle. a Quick shake of the bottle revealed the bag was still in there but it was the one placed between the walls of the bottle so no chance of getting it out. A new bottle was sourced from GSF as they had a deal on but in hindsight i should have ordered it from Germany and just paid one lot of postage. Coolant system was flushed out with the hose pipe until it ran clear and left to drain.
Moving inside the car i removed the glovebox which was very tricky but i later watched a youtube video and it could have been a lot easier but i got it out with no damage and all of my skin still on my fingers. The side trim for the centre console was removed, one t20 screw and the panel just unclipped. there was a foam trim under the heater motor that was held in with two plastic wing nut type screws this came off to reveal the heater motor that needs to come out to enable the matrix to be removed. The motor is held in with 3 t20 screws and there are two clips that need easing away to enable the heater to drop down but before this you need to unplug the power connector underneath. Sorry forgot to say before the heater motor comes out there is a heater vent that directs air to the passenger feet, this needs to come out and there is one t20 screw that holds it in, the screw faces you just by the fusebox, once this is out you have to contort the vent out after pulling it free of the heater box. It was a bit fiddly but it came out ok.
With all these parts out if you look towards the centre console side of the dash you will see the heater matrix pipes. covering the heater matrix is an oblong black cover held on with 3 t20 screws. the screws need removing and there are 3clips that also secure the panel. I covered the floor area with a plastic sheet to contain any leaks from when the matrix pipes were removed.
The pipes are secured by a clip and a clamp. the top pipe has a clip that has a locking tab that needs to be lifted before the clip can be slid backwards to remove. The bottom pipe has a clamp that is held together with a 3mm allen bolt. Before removing the pipes there is a plastic piece that bolts to the transmission tunnel (it's what the t20 screw that holds the centre console trim screws into) peel the carpet back and there are 2 10mm nuts that need to be removed. Once this is out of the way it gives more movement of the heater pipes as they need to be moved to enable the matrix to slide out.
A quick tug on the pipes frees them from the matrix along with 200ml of coolant ( i had an old ice cream tub on hand to catch as much as i could). Once the pipes are removed you can then unclip the oblong cover that covers the end of the matrix. It has a green seal all the way around presumably to help seal the air into the heater box. As stated earlier the pipes need to be jiggled around and the matrix should slide out towards the heater motor housing, it will hit the housing but then a slight movement downwards will let it come past and the matrix is out.
I looked inside and could not see any blockages but when i filled it with water it did not flow very well. Fitting the new matrix is basically a reversal of the procedure above. things to be careful about are: when sliding the new matrix back in be sure to get your head right up behind the matrix to make sure the top pipe is not fouling the fins on the back of the matrix as this will hinder it going back in. The new matrix i got seemed a little tighter to fit than the old one that came out but i took my time and made sure it went in evenly to make sure it was fully home. remember then the oblong cover needs to go on before any pipes are fitted. I cleaned the pipes and re used the old o ring seals and just put a tiny smear of rubber grease on the o rings which helped them slide back into the new matrix part number of the seal and clamp kit is 5Q0-898-400-A same part number whether sourced from VW SEAT or SKODA but VW are the cheapest at £5.51 whereas Seat and SKODA wanted £9.91!! getting the top clip on for the pipe was easy but the bottom one gave me a bit of pain. I think because it was slightly out of round where i had removed it but i took it back off and fitted it to the old matrix to make sure it was shaped properly.
After all this i refilled the coolant and what i am about to type may not be to everyone's liking but i filled the coolant with G12 as it's what we use on the commercial vehicles we repair that have aluminium radiators. Also we run a fleet of VW caddy vans and i checked our 67 plate caddy that has the same engine as my octavia and the coolant tank on the caddy states G12??
Unfortunately i did not get any pictures but there are videos on youtube of this repair being done. Book time is 1.4hours, probably doable if you worked at skoda but i would allow 3 hours to comfortably do it. like most things if you take your time and watch youtube so you have an idea of what is involved then doing the matrix on one of these is not a scary prospect. Tools wise i used
T20 screwdriver
10mm socket and ratchet
1/4 drive ratchet with T20 bit for rearmost heater motor screw
Flat blade screwdriver
3mm allen key
Torch and that's it!
Heater now works a treat with heat evenly at both sides.
Hope this helps