Brake pad on new bike

Referring you to my comment, some more information would let us be more helpful. But, some general information: Brake pads for rim brakes are typically a rubbery material mounted perpendicular to a post. That post is fixed to the brake mechanism by some sort of mount that allows up-down and side-side movement when loosened. The pad should rub on the rim, as you noted, not the tire when the brake lever is pulled by the rider. So, a general procedure:

1. Find a way to hold the brake lever so the pads are almost touching the rims. If you know how to use barrel adjusters, do so. If not, a Velcro strap holding the lever down while you work will help.
2. Adjust the mount holding the pad so that the rubber is nicely squared on the rim and no longer touching the tire. Tighten the mount again.
3. Release the lever.

As mentioned, this is a very general procedure, based on a lot of assumptions. More information or a couple of photos would let us give better advice and point out any potential gotchas. This can require some patience as you tweak it just right.

Noodle: the metal pipe that turns a V brake inner cable through 90 or 130 degrees to go to the handlebar brake lever.

To disconnect or reconnect the brake's noodle you would squeeze the end of both brake arms inward toward each other. This presses both brake pads into the rim.

If you can reach, hold them in place with your secondary hand, and use your dominant hand to install or remove the noodle from the flippy arm bit.

^{From https://www.chicagobikeblog.com/blog/2014/2/20/how-do-you-get-the-dang-wheel-out}

There is not a lot of slack to do this; it should be a close fit. The rubber boot just slides out of the way, and when you release the brake arms, they will pull themselves away from the rim (allowing the wheel removal.)

Given that you already have something wrong with the brake setup, it may not be able to get the noodle in/out because of the brake pad being mis-positioned. Or the wheel may not be installed completely right, also blocking things.

If its a brand new bike, most bike shops offer a ~6 week tuneup/service for new bikes sold. Check with your supplier. This is one feature missing if you bought the bike on-line.