How to obtain values for chlorophyll a in SNAP using Sentinel 2 MSIS2A or MSIL1C products?

I am trying to obtain chlorophyll a data from Sentinel 2 images in SNAP. I am using the following steps:
Raster>Geometric Operations>Resampling>10m, then Optical>Thematic water processing> S2MCI processor
in the processing parameters I have two options: S2MSI L1cMCI and S2MSI L2MCI. For the image I use MSIL2A both options are acceptable (but using different mask expressions). Hereafter RGB image is giving different results in color expression, so here is my confusion.
Which color have higher values of chlorophyll - the red or the green?
Nothing happens in the pixel info, how should I retrieve the pixel values?
Are there some manuals for further processing?

Honestly, I don’t understand what you want to do.
After processing MCI, the resulting product has a band “MCI”. This one gives you the values for the chlorophyll index. An RGB image does not give you much information about chlorophyll.
For S2, the RGB is usually made as R=B4, G=B3 and B=B2. So you can open these bands individually and inspect them. Then you can see which one corresponds to higher MCI values.

Although you gave me very precious and helpful information. As you wrote, the MCI band contain the pixel value, so thank you a lot!
the pixel values in MCI band are in (dl nm-1). Is that delayed luminescence? How to convert them into standard units (mg/m3)?

“dl” stands for “dimension less”. The band has no unit. MCI does compute chlorophyll, it is just an indicator for chlorophyll. I’m not aware of a conversion to chlorophyll concentration. In the help of the processor the algorithm is explained and papers are linked.