You shouldn't use the uses ... in ... if you can avoid this and use the Unit Search Path instead (Project Options -> Paths -> Other Units (-Fu) or something similar, I don't use the english IDE, just translated it on the fly).
The reason for this is simple and does not even have anything to do with bugs in relative paths or similars what was discussed earlier. It is simply that when you change the locations, e.g. restructure your directories, you only have to change one place, the project options, not have to go through every single unit to change the uses paths. Also if you are using multiple units from the same directory, or you are using the same unit in different units, you do not have to do the same work twice, writing the whole path in the uses clause, but can just write the unit name (and auto-complete will even assist with that).
Writing paths manually in the uses is just going to make your life harder, and has not really an advantage.
That said, one slight inconvinience withe Lazarus is that if you are using Build Modes, adding a new path to one build mode does not add it to the others. A popup with information like: "You added Paths to the search path, do you want to also add them to the other build modes" would be really helpful. Had the problem quite often that when building release mode, I first had to add all the new paths to units I had added during development.
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