Do you mean an open challenge (like one found on http://www.chess.com/echess/open_invites.html) or one addresed specifically to you?
accepting a challenge

Assuming you are talking about on-line turn-based chess (not live chess) then you click on online chess. You will then see your current games. Below that you will see challenges that you have received. You should click view for the one you want to accept and then accept. Of course, you may not have any challenges. In that case, you can go to online chess and look at the top right of the screen. You will seek a link called Open Seeks. Click on this and you will see a number of general challenges where people are seeking playing partners. View and accept these in the same way you would accept a challenge made to you.
You can also consider creating a new seek yourself so that you are issuing a challenge to people generally. Or join a tournament!!!

Once you are logged into the Live Chess you should see a "seeks" tab where you can open other player's open game challenges. Also, if someone sends you an individual challenge in the Live Chess you should automatically see a link come up to accept or decline the game challenge.
No it is not recent. The link above does not exist. Its not called seeks, its called open challenges. and for short games, going to live chess (under "play") works. But for correspondence games (1 day+) I still can not find the link to open challenges.

Can somebody help me with this? me and a friend have been confused trying to play together when he does play against friend and does something other than a daily game.

Once you receive a challenge, there will be a board icon on the top right, click it to accept.
On the mobile app, there will be a banner along the top. If you do not receive the challenge, either your settings for receiving a challenge have been adjusted or your friend may need to resend.
Its cool to be comment #14 on a form that was posted in 2009. 😎
How do you accept a challenge?