What is the best way to transport process chains to test system? 
I got many other additional and unwanted objects got collected when I tried for collection of process chains from transport connection. 

To transport a process chain the best is to transport only objects created for the process chain. On my system I created specific obejcts for PC : Infopackages, jobs, variant. those objects are only use for PC. By this way I avoid errors when users restart load or job manually. 

So when I want to transport a process chain I go in the monitor and select the PC make a grouping on only necessary objects, and I go through the tree generated to select only what I need. Then I go in SE10 to check if the transport contains not other objects which can impact my target system. 

You can avoid some uncessary objects by clicking in Grouping > Data flow before & Data Flow After . For example you already have infopackages in your target system but not process chains & you only want to transport only process chain without any other objects like transfer structure or infopackages . You can choose before or after option .  
 

You can also choose hierachries or display option from the Display tab too if you have objects in bulk but make sure all object are selected ( in case when different-2 process chain having different kind of object then better use Hierarchy, not list ) 

While Creating these TR some objects may be in use or locked in other TR so first release them by Tcode Se03 ,using unclock object ( Expert Tool ). 

These options can reduce your effort while collecting your objects , even after so much effort you get some warning or Error like :- objects are already in system then ask basis to use overwrite mode.