I have received quotes from 3 roofing companies for a complete roof replacement. Two are similar and one differs quite a bit. My roof is two levels, has three skylights, 2 dog house dormers and one larger dormer (400 sq ft) with a low slope roof. I have decided on using 50 year asphalt shingles.
Two companies said they would mechanically attach EPDM to the low slope roof area and one said they would glue it. Which is the best method to apply EPDM?

Two companies said they would apply water/ice shield 12" at all flashing walls, one company said they would not apply it at the flashing walls, and only apply it on the eaves. Is it necessary or highly recommended to apply ice shield at the flashing walls?

The company who said they would glue the EPDM and not apply the ice shield at the flashing walls has a lifetime warranty on leaks and repairs while the other two companies have either a 5 or 10 year warranty. All companies are well established with many references. I want to replace my roof once the right way with no headaches. Is it best to go with the longest warranty or should I go with the shorter warranty with the mechanically attached EPDM and the additional snow/ice shield?