With the HUD chip equipped, you’ll have no problem finding the fragments assuming your scanner is in range to locate them. To make things easier, you should build a scanner room and search for components.
Each component will have fragments dotted about in various areas, so you’ll need to prepare for a bit of exploration. The Cyclops is no different, requiring three scans of three different components before you can build the submersible. In Subnautica, you must scan fragments of damaged bits of machinery in order to unlock blueprints.