Question 1:
Pen and markers contain ink/pigments and they will seperate as components along with what you are tring to identify, contaminating the sample. Pencil graphite will not.
Question 2: I am not sure I understand the question the way you have it written but, the spot to be analyzed needs to be above the solution, on dry paper so the solution can "crawl" upward and catch each component in the sample. You are not "washing" it, you want the different components in the spot to be analysed to be drawn up through the paper.
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