So you messed up your silicone job. Take a razor blade, peel off the silicone and try again. We all learn from trial and error and with practice we all get better at our craft. I'm not sure about the details of your DIY formicarium but if you are attaching two unwieldy pieces that you cannot use c-clamps on, using scotch tape to hold the pieces together while the glue works will help. You must give the silicone time to cure and harden, depends on temp and moisture (24-48 hours is okay). A caulk gun will help you apply silicone much better if you are not using one(?) and if your outworld is big enough, you can use a gloved finger to compress, clean and apply even treatment of the silicone. Any mineral spirit/vinegar/paint thinner/etc. will help clean up residue before and after.
I mean, it probably took you less than a minute to apply the silicone, right? Why not take this opportunity to learn from your mistake and do it right this time? There are many tutorials available online on how to properly do 99% of anything an ant keeper would want to do.
On the other hand silicone will bind to silicone very nicely. If your hole truly is just a small one, why use a different material to repair the hole? Just clean the area to bond, use the same silicone and give it time to work.