the joined wires you mention are probably for things like fuel relay power, perm live, ignition etc which are tapped into from several places.
ETKA is for parts, if you want diagrams its ElsaWin you need. which I have
look in my signature link for 6x0aucecu.pdf, that should cover what you need. The octavia loom will probably be the same as the equivalent code VW/Audi ecu loom, see my sig and my wiring guide above.
the bad news is its not a DBW type ecu with a 80 pin ecu plug, so all the pins are different. you'll have to cut the wires off the old ecu then tap to the new one. The good news is as long as the wires are thin enough you dont need a terminal tool to remove the old pins or to crimp new wires into the DBW ecu terminals. Slide out the purple retaining tab on the end then the pin holders pop out. Pull the rubber seals back then use a pick tool to release the tab for the wire you need to work on, cut the wire off and pull it out and bin the pin. Swap over one of the many spare pins VW thoughtfully left for you in the empty positions then use something suitably blunt to push the new wire into the pin jaws. You'll see what I mean! If you've ever terminated a/BT type phone socket you'll know the score.
or just cut n splice where necessary, whatever works. just be sure to stagger your joints so they dont bulk out the loom or rub thru