1. You technically can pay multiple years at once, but, in your situation, it may not be a good idea. Your 2017 amendment may take up to 16 weeks to process so if you overpay on your account when you file your 2018 taxes, the IRS is likely to refund you that money since your amendment would not have posted already. Its cleaner to pay 2018 when you file and then pay for 2017 when you send in your amended return.
2. You cannot e-file an amended return. You can still prepare the amended return using the 2017 CD - you just need to print and mail the return. If you owe money, you can just send a check with the amended return or go online at IRS.gov and make the payment.
