When you recruit the first new member, new options regarding the organization will appear. By holding down the guild button you can choose the functions which the new recruits will realize or enter the mission screen. The first option lets you choose between assassination and riots. Both can be launched by pressing the guild button. By choosing assassination you can murder a designated target, while the second option lets you start riots which will draw the attention of guards. You can learn more skills by recruiting new members.
The mission screen is used to send recruits onto different kinds of missions. Completing them gives them experience and lets Connor get useful items and gold.
After completing a mission in a given area, you will be able to complete further ones and eventually completely take over the territory from the Templars. Regained areas will provide Connor a constant income. When choosing missions, note the difficulty level marked by the amount of stars beside it. The higher it is, the more experienced recruits you will need to complete it. The percentage chance of success will be displayed as you assign assassins to a given errand.
In order to ensure a high cash inflow, it's worth to complete as many missions as possible. You however have to remember that assassins on missions become inaccessible for some time and can't help you during your fights in Boston. If you want to gain full district synchronization, you need to unlock all recruits and get them to level 11.