Bring boiling-water canner, half full with water, to simmer. Wash jars and screw bands in hot soapy water; rinse with warm water. Pour boiling water over flat lids in saucepan off the heat. Let stand in hot water until ready to use. Drain jars well before filling jars.
Remove colored part of peel from oranges and lemons using vegetable peeler. Finely chop or grind removed peel into thin slivers; set aside. Peel and discard remaining white part of peel from fruit. Chop fruit pulp, reserving any juice; set aside.
Place fruit peels, water and baking soda in large saucepan. Bring to boil on high heat. Reduce heat to medium-low; cover and simmer 20 min., stirring occasionally. Add reserved fruit and juice; cover and simmer an additional 10 min. Measure exactly 5-1/2 cups prepared fruit into 6- or 8-qt. stockpot.
Mix 1/4 cup of the sugar and pectin in small bowl. Add to fruit in stockpot; mix well. Add butter to reduce foaming. Bring mixture to full rolling boil (a boil that doesn't stop bubbling when stirred) on high heat, stirring constantly. Stir in remaining 3-3/4 cups sugar. Return to full rolling boil and boil exactly 1 min., stirring constantly. Remove from heat. Skim off any foam with metal spoon.
Ladle immediately into prepared jars, filling to within 1/4 inch of tops. Wipe jar rims and threads. Cover with two-piece lids. Screw bands tightly. Place jars on elevated rack in canner. Lower rack into canner. (Water must cover jars by 1 to 2 inches. Add boiling water, if necessary.) Cover; bring water to gentle boil. Process 10 min. Remove jars and place upright on towel to cool completely. After jars cool, check seals by pressing middles of lids with finger. (If lids spring back, lids are not sealed and refrigeration is necessary.) Marmalade sets slowly and may take up to 1 week to set completely.