I just started my seedlings about 3 weeks ago. My friend planted his differently than mine, and his has already started it's first sprout. Not thinking, I planted my seeds at the bottom of the pots then put the soil on top of the seeds. Would that cause a problem for the seeds to start growing? I was thinking I should turn them over so that they are closer to the top of the soil. But can I do that? Or will it cause even more harm to the seeds?
After 3 weeks you might as well get new seeds. Then read the package on how to grow them. You are way to early, because tomatoes should only be 6 to 8 weeks old when you set them out. That would be early March, much to early even in IN.
You planted your seeds way too deep where they won't have a chance to sprout, and since they've been buried like that for 3 weeks it's likely too late to save them so your best bet would be to get some new seeds and try again. Next time read the instructions on the seed packet--it will tell you how deep to plant the seeds. Some seeds get planted a little deeper than others, but none of them are going to want to be buried at the bottom of the pot. I suppose you have nothing to lose by taking the seeds out and replanting them at the proper depth though so if you want to try that first you'll just lose a little bit more time. If the seeds are mushy and moldy though there's no chance they'll sprout so you should toss them.
CG's other point is that assuming these are seeds for flowers or vegetables that you want to plant out in your garden in the spring, you should also read the packet to see how long before your last frost date you should start the seeds. You don't want to start them too early because then they'll be ready to plant outside too early and they'll get zapped by frost. Here's a list of when would be the right time to start a variety of different vegetables indoors http://www.almanac.com/gardening/planting-dates/IN/Indianapolis But if you're growing something not on the list here, read your seed packet.
Just out of curiosity, I would carefully dump out a pot & see if the seeds show any sign of germination at all. If they are buried too deep, the leaves can't sprout but the first root might try. Just curiosity, you don't have to dump the pots out - You should be able to put new seeds in the old pot as - just not so deep!