Hello,

I am setting up a Mikrotik box to do traffic shaping and then per customer rate limiting. Following the examples on the wiki page I am going to mark traffic for shaping in prerouting and prioritize in global-in, then remark traffic in chain forward and rate limit in interface queue. My question is for the first marking should I mark the connection and then mark the packets in prerouting for the first shaping and then remark the connection and mark the packets in forward for the limiting, or should I just mark the packets in prerouting and then mark the connection and remark the packets in forward?

Are there any issues with marking a connection once (say dst port 80 for http) in prerouting then remarking the connection by customer ip in chain forward?

There are no issues remarking a connection at any time, the original mark will simply be overwritten.
Whether you mark the connection or just the packets depends on what your ruleset looks like, but generally speaking the router performs better if you mark a connection and then perform other actions based on the connection mark (which requires checking only that one parameter for each packet) rather than checking each packet for several parameters (interface, protocol, destination port etc.)

I am a beginner, can you give me some examples.