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Hi dear,
Yes you can fill up counselling at both places. Both JEE mains and MMMUT are separate entities so there counselling process is also different. Appearing in JEE mains counselling you can be given various choices of colleges which accept JEE mains score for admission. Appealing in MMMUT counselling only gives you choice to get admission in Madan Mohan university. So you should appear for both counselling.
All the best
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