I too had to figure this one out when I put in the e-pump. My answer will be based on the attached picture of the FSV on my truck. Keep in mind, this is a '92 F-350. Other years may possibly be different, but I don't think they'll vary too much.
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Don't know why that got turned 90°. The top of the picture is toward the front of the truck, so bend your head to the left. IE, rotate the picture 90° clockwise.
That's the FSV, mounted on the frame rail, near the front fuel tank (you can see the corner of the tank). The two lines going forward are coming out the top of the FSV (to the left as the picture sits). The engine feed is the one closer to the frame, and the return is closer to the fuel tank. So, as they exit out the top of the picture, the return line is to the left, and the feed line is to the right.
If you pull those lines off the FSV, be sure to have some new clips on hand. You'll probably break the existing clip. Remember, pull the clip out, then pull the line off the FSV. The clips are Dorman part number 800-015.
If you need me to re-orient and/or label the picture, let me know.
Hope that helps.
Edit: I didn't realize, looking at the thumbnail picture, that I had labeled things. That may help too.