When you order, select the Custom DNA Oligos option. At the bottom of that ordering page you will see tabs that say 5' Mods, Internal Mods, & 3' Mods. Most modifications are not available at the 25 nmole scale, so if you do not see the modification you are looking for you should increase your synthesis scale to at least the 100 nmole scale. This will increase the menu of modification options available. When you find the modification you would like, click on the "Add Mod" button to the left, and it will add the appropriate modification code to your sequence. If the modification is internal you will want to make sure that the entire modification code inserted into the exact position desired within the sequence.
Decoded article on ordering modified oligos can be found at
Ordering Modified Oligos