Stains on toilet paper do not render you niddah as long as you waited at least a few seconds after urinating before wiping. Please read our article on toilet paper for further details.
Unfortunately, even if the stain on the toilet paper did not render you niddah, the stains on the bedikot may have and you need to bring them to a halachic authority for evaluation. For this reason, we recommend that a woman should not perform any bedikot besides those that are halachically mandated (such as hefsek taharah, during shivah neki’im, on onah days.) A bedikah can not “undo” a questionable stain, and can possibly make matters worse, since stains found on an internal bedikah are treated more stringently that stains found externally.
If the halachic authority says the stains found on the bedikot make you niddah, then you need to wait five days from when you did the bedikot before counting the shivah neki’im and immersing.
If however, the stains on the bedikot were acceptable, you should take precautions against becoming niddah from further staining, as outlined in our article on staining.
Please feel free to get back to us with any further questions.