The marks on the covers are always for 0*BTDC. The crank pullies, however, have different marks for different engines based on their specified base timing. I always match base timing to the head design, unless radical changes to the head chamber volume have been made.
A6 crank pulleys have the middle mark at 18*BTDC.
Z6 crank pulleys have the middle mark at 16*BTDC.
Y8 crank pulleys have the middle mark at 12*BTDC.
All D16 and D15 (and I am fairly sure that all D-series engines) have the same timing marks on the oil pumps and covers, as they are all indexed from the TDC position of piston #1.
You will want to set the base timing in your ECU to match the base timing mark (middle of the three clustered marks) on the crank pulley you are using. Since you are using a Y8 head (an assumption based on your stating that you are using a stock Y8 cam), I would recommend sticking with 12*BTDC as your base timing. If you are using an A6 or Z6 crank pulley, you will have to scribe new timing marks on the pulley. This is easily done with a good set of dividers. Set the dividers to match the distance between the clustered marks. Each one of those marks denotes 2 crank degrees. For an A6 pulley, the stock marks will be @ 20*, 18* and 16* BTDC. To get to 12*, you will want to scribe another 3 lines TOWARDS the 0*BTDC mark on the pulley. I also recommend making a small notch on the pulley with a triangle shaped needle file. This will always show up on the crank pulley with a timing light. and is very easy to feel for, more so than the stock lines. If you have a Z6 crank pulley, you would do the same thing, except that the Z6 crank pulley marks are at 18*, 16* and 14*, so you would only need to scribe a further 2 lines and notch the 12* line.
I would also recommend using a Y8 crank pulley. They are a much superior design, IMO. Yes, they are heavier, but in the cases of all the pulleys, the mass is nearly centered and it does not effect the rotational inertia too much. The reason why I suggest using the Y8 pulley is because it is a much more modern update and should dampen harmonics much more effectively.
Since I don't know what the base timing is set to in your bin, I can't offer any insight into what is going on with the ignition timing, but I can only strongly suggest that you ensure that the base timing in the map matches the base timing set with the distributor in order to ensure that the timing you are changing in the timing maps has the desired effect. Running with the timing centered on the A6 pulley with anything other than 18*BTDC as your base timing is going to lead to an unintended ignition advance of the amount of the difference between the bin timing and physical ignition timing.
I hope that is all clear enough.