Can't really answer that without seeing your factory first.
If you use the train, it's usually for travelling over very long distances. So if you build installation requiring frequent modification on both end you'll have to travel by train frequently. If you want to spare yourself some comutes, it might be preferable to :
1) ship fully finished items to a special plants where you won't be going often (ex : control rods and encased steel beams to a far away nuclear factory + plant)
2) ship the most basic ores to your main factory (delivering iron, copper, quartz, etc) to keep the maximal flexibility of production at your main factory
But maybe your main factory is already huge and packed, you'd have more space around your distant stations.
And maybe you want to be able to shut down every distant machinery by disconnecting the train station, savingpower for your main production site just by removing a cable instead of travelling everywhere.
Or maybe you just follow a roleplay story and you deliver ores and ingots because of historical reasons.
What's best depend of you.