Embodiments of the present invention provide systems, devices and methods for managing skew within a polarized multi-channel optical transport system. In a DP-QPSK system, skew between polarized channels is compensated within the transport system by adding latency to at least one of the polarized channels. The amount of added latency may depend on various factors including the skew tolerance of the transport system and the amount of skew across the channels without compensation. This latency may be added optically or electrically, and at various locations on a channel signal path within a transport node, such as a terminal transmitter or receiver. Additionally, various embodiments of the invention provide for novel methods of inserting frame alignment bit sequences within the transport frame overhead so that alignment and skew compensation may be more efficiently and accurately performed at the transport receiver.