There can only be one Auto increment column, but it can be any. I'm assuming it's currently your PKEY field, so removing it will mean you need to manually create a unique PKEY to keep it as your primary key.
alter table tablename modify PKEY int(11) unsigned NOT NULL;
alter table tablename add index (USERID);
alter table tablename modify USERID int(11) unsigned NOT NULL AUTO_INCREMENT;
ALTER TABLE tablename AUTO_INCREMENT = 1000;
a fresh create would look like this:
CREATE TABLE `foo` (
`PKEY` int(11) unsigned NOT NULL,
`USERID` int(11) NOT NULL AUTO_INCREMENT,
PRIMARY KEY (`PKEY`),
KEY `USERID` (`USERID`)
) ENGINE=InnoDB AUTO_INCREMENT = 1000;
However, I'd recommend you make USERID a primary key