After the merge operation is finished it is possible to have some resources in conflict. This means that some incoming modifications for a resource could not be merged with the current modifications from the working copy. If there are such conflicts, a dialog will appear presenting you the resources that are in conflict and from where you can choose a way in which every conflict should be resolved.
The options to resolve a conflict are:
Resolve later - used to leave the conflict as it is for manual resolving it later;
Keep incoming - this option keeps all the incoming modifications, discarding all current ones from your working copy;
Keep outgoing - this option keeps all current modifications from your working copy, discarding all incoming ones;
Mark resolved - you should chose this option after you have manually edited the conflict. To do that, use the Edit conflict button, which will bring to you a dialog presenting the conflicting resource's content for current working copy version and the one with the incoming modifications. After manually resolving the conflict, the resource will be marked as resolved.