The Missing Link stands apart as an episode by itself, even though the timeline in which is happens is during the main story;
During the main plot of Deus Ex: Human Revolution, there’s a point near the end during which you climb into a pod in order to get to the Panchea complex. When Jensen climbs out of the pod on the after arriving, Pritchard mentions that you've been out of contact for three days.
The Missing Link doesn't affect your main story progress, you can feel free to play around with any Praxis Points you come across and it won't affect any progress on any achievements you've been working on in the main Deus Ex story line as it isn't integrated into the main campaign.
Update (credit to Diziet): Certainly would recommend not playing 'The Missing Link' until the point in the game detailed in the spoiler.
In Deus Ex Human Revolution: Director's Cut, the Missing Link content is built into the main story and does directly effect your main story progress (including Foxiest of the Hounds and Pacifist).