Hello Khem,
Please find the answers to your questions below.
1. You have to use a culture medium, where you normally culture your cells. Make sure to monitor the cells periodically because clonogenic assays lasts for more than a week (depends upon the growth kinetics of the cells) and the media might evaporate by that time. So you need to periodically replenish or change fresh media (media change is preferable).
2. You can use any cytotoxic agent of your interest. However, I would recommend to use non/sub-toxic concentrations of your agent because you will seed only 500 - 1000 cells per well in a 6 well plate and because of the cell-drug ratio, toxic conc. of your compound might kill all the cells in a short period of time. Infact, control cells treated with vehicle (same volume as your treatment) might not form colonies. The results will then be inconclusive with loose ends.