We have 4000 transports...would like to know the best methods of transports

We have 4000 transports...would like to know the best methods of transports.I understand mass transports and consolidation of transports through transport organiser can be of help ..However would like to understand more on the following points

1)In both the cases, how dependencies between transports will be managed.

2)How Sequencing will be managed?

3)Which is recommended and under what circumstances?

4)Pros and cons of each?

Thanks

Shamna