First of all you need to fold your fabric properly. Fold it in half lengthways, matching up the selvedges. Don't forget that the right sides should be together, as you'll mark on the wrong sides. Usually the right and wrong sides are quite obvious: they have a different texture, wave and even color. Right side is usually brighter. 

Once you've done this step, let's move forward.

Place your pattern piece and fix it with pins. Mark all the alterations. Don't forget to include the seaming allowance.

Start removing pins, one by one, and immediately pin both lawyers of fabric together right on top of the marking line. Pay a special attention to all edges.

Don't forget to pin detail on a folding line.

When you'll finish, turn your detail to another side and start pining a pattern piece. It'll be much easier because you'll see where exactly you need to place your pattern - you'll have a perfect contour, formed by pins.

After pinning your detail, don't forget to remove all the pins from the already marked side - it'll make the marking process easier, so the tailor's chalk doesn't stop at the pins.

How do you mark alterations on a folded fabric?