What you have up there now are just roof rack 'deletes', strips that have the holes underneath where an OEM rack would bolt on. My SR5 came with these but I just found an OEM rack at a parts yard for $80.00. You just unbolt the deletes and bolt the rack rails on. Onto the rack rails go three bars plus two cross bars where you'd attach your cargo (box or basket or whatever).
I'm pretty certain Yakima makes a fit kit for the OEM rails (not the deletes) so you'd need to at least find some rails. Otherwise you can purchase a rack that goes into your gutters but that will sit forward on your roof and not in back which is the preferred position.
Here's how mine looks now with the OEM setup - sorry for the miniscule photo!
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1999 SR5 3.4 V6 4WD | Desert Dune Metallic | Big City Weekdays & Back Country Camping Weekends
265/75/16 Goodyear Wranglers| Bilstein HD Shocks | OEM 'Tall' Springs | Hella 500s | Clear Corners & Signals | Cobra CB | Rust