You should be fine. The fuse is a 250 or 300 amp fuse used as a catastrophic failure device. It will still blow if it is 5 feet away from the batteries.
However, the 5 feet of wire is not protected. If this section of wire shorts, it will continue to be a short after the fuse blows. Use wire loom and secure it well for extra protection on this section of wire.
Edit: After re-reading your post
Thinking about it, if this section runs under your bed and shorts it could be a big problem (fire). Forget what I said above. Put the fuse on or near the battery tray to protect the entire circuit.
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