Hello @kamalwolly
The usage of the S32CT/EBT allows you to access all the MCU settings and it generates the configuration files.
For each pin muxing, in the case of S32CT, you shall use the graphical pins component as shown below (while for the EBT is the Port component). The Pins component can be opened by pressing the first button on the top right-hand side. From this component, you can assign the pins to each peripheral according to your application requirements. For example:

The next step is to enable the channels you want to convert in the Adc tab, as you already showed us in the picture.

Before going further, I shall mention that the MBDT for S32K3 generates code on top of the RTD functions. And there are two types of functions in the RTD: the ones described in the ADC AUTOSAR API specification of the standard MCAL layer(e.g. Adc_StartGroupConversion), and the additional ones designed to cover the extra functionalities of the hardware, like the ones handling the BCTU.
The channels you are adding will not be displayed in our toolbox because the API for the conversions deals with groups. Instead, the channels have to be added inside a group, and you can start conversion for a particular group (please see the s32k344_adc_single_read_s32ct example) even in particular one group can contain only one channel.
Because you have mentioned that you want the BCTU to start the conversions, well, I strongly suggest starting by our s32k344_adc_ctu_ebt. Since the 1.1.0 release, you can open, see how the blocks are being used to trigger such conversions, even you don't have EBT installed. You shall enable the ADC to be controlled by the BCTU using the Adc_EnableCtuControlMode, then you start the conversion of a particular trigger (of course, set in the S32CT).
Each trigger can command either a LIST or a single channel and can store the results either directly in the BCTU_ADC_Data_REGs or inside some FIFOs. In case you are using lists, then you can convert up to 3 channels at the same time, of course, if they belong to different ADC HW instances.
For example, in the below settings, the internal Trigger 2 stores the results inside the ADC Data regs, and starts conversion for a list, on the instances (ADC_2 and ADC_1, because of the Adc TargetMask being 0b110 - on the ADC_0 is disabled) starting from the Conversion List Index 0.

The Bctu List can be seen below. It will start the ADC_2 CH S10 and the ADC_1 Channel S19, and then the triggers will stop, because of the second idem marked as "Last channel"

Unfortunately, for understanding the error's source, you have to send me the entire log. The build process creates multiple threads to build sources files in parallel, so the error is somewhere in the log above the part you have attached to us.
Regards,
Marius