Emerging lightweight cloud technologies, such as Docker containers, are gaining wide traction in IT due to the fact that they allow users to deploy applications in any environment faster and more efficiently than using virtual machines. However, current Docker-based container deployment solutions are aimed at managing containers in a single-site, which limits their capabilities. As more users look to adopt Docker containers in dynamic, heterogenous environments, the ability to deploy and effectively manage containers across multiple clouds and data centers becomes of utmost importance. In this paper, we propose a prototype framework, called C-Ports, that enables the deployment and management of Docker containers across multiple hybrid clouds and traditional clusters while taking into consideration user and resource provider objectives and constraints. The framework leverages a constraint-programming model for resource selection and uses CometCloud to allocate/deallocate resources as well as to deploy containers on top of these resources. Our prototype has been effectively used to deploy and manage containers in a dynamic federation composed of five clouds and two clusters.