How does Ubsoft's app "ctOS mobile", work from the main Watch_Dogs player's perspective?
The person playing Watch_Dogs on PC/PS/XBox gets an on screen prompt indicating that somebody is challenging them.
This prompt is only possible outside of missions, like the Fixer missions. Online modes only become available after completing the first few story missions up to and including the Online Contracts Introduction (which is when you first go through the tutorial for the one on one hacking missions).
You can only interact with other player games by "intruding" another player for a hacking mission or a race or any other of the available intrusion types. When you are hacking someone else's game, their job is to stop you from doing so, therefore all the hacking you do in their game has no confirmations.
The online modes are available few missions into the game when you get "hacked" by an AI player as a tutorial. Online interactions can be disabled within the options if so desired.