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Originally Posted by cyrnel
Because an IDE bus can only handle one request/response at a time, any request to any target ties up that channel until the target responds. The difference with optical drives is that their response time is much slower than hard drives. Drivers and apps can use asynchronous techniques to minimize spin up and seek blocking but without a huge cache they'll never match the response times of hard drives.
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In other words, it'll only be an issue when you're actually USING the optical drive. It's not like the drive will just simply BE SLOWER because it's sharing an IDE line with the CD-ROM.
I'd put Linux on the 40gb unless you think you'll be using the CD a lot (frankly, after install, I almost never touch my CD drive). You could also partition the 200gb to have say 20gb for a ext3 partition for Linux and the rest a ntfs partition for file storage. 20gb ought to be an ample plenty, with the rest available for big file storage.