Please have a look at the changes I made in do_show and do_confirm in the confirmations_controller.rb (Related question: https://groups.google.com/forum/#!topic/plataformatec-devise/4amIRvFCcxY)

confirmations_controller.rb

# /app/controller/confirmations_controller.rb
class ConfirmationsController < Devise::ConfirmationsController
  skip_before_filter :authenticate_user!

  # PUT /resource/confirmation
  def update
    with_unconfirmed_confirmable do
      if @confirmable.has_no_password?
        @confirmable.attempt_set_password(params[:user])
        if @confirmable.valid?
          do_confirm
        else
          do_show
          @confirmable.errors.clear #so that we wont render :new
        end
      else
        self.class.add_error_on(self, :email, :password_allready_set)
      end
    end

    if !@confirmable.errors.empty?
      render 'devise/confirmations/new' #Change this if you don't have the views on default path
    end
  end

  # GET /resource/confirmation?confirmation_token=abcdef
  def show
    with_unconfirmed_confirmable do
      if @confirmable.has_no_password?
        do_show
      else
        do_confirm
      end
    end
    if !@confirmable.errors.empty?
      self.resource = @confirmable
      render 'devise/confirmations/new' #Change this if you don't have the views on default path
    end
  end

  protected

  def with_unconfirmed_confirmable
    original_token = params[:confirmation_token]
    confirmation_token = Devise.token_generator.digest(User, :confirmation_token, original_token)
    @confirmable = User.find_or_initialize_with_error_by(:confirmation_token, confirmation_token)
    if !@confirmable.new_record?
      @confirmable.only_if_unconfirmed {yield}
    end
  end

  def do_show
    @confirmation_token = params[:confirmation_token]
    @requires_password = true
    self.resource = @confirmable

    # added to enrich the confirmation form
    @company = Company.find_or_create_by(domain: Mail::Address.new(@confirmable.email).domain)

    render 'devise/confirmations/show' #Change this if you don't have the views on default path
  end

  def do_confirm
    @confirmable.confirm!

    # added to update other models on confirmation
    user = User.find(@confirmable)
    company = Company.find_or_create_by(domain: Mail::Address.new(@confirmable.email).domain)
    company.name = params[:user][:company_name] if company.name.nil?
    if company.admin.nil?
      company.admin = user
    end
    company.save

    user.first_name = params[:user][:first_name]
    user.last_name = params[:user][:last_name]
    user.employer = company
    user.save

    set_flash_message :notice, :confirmed
    sign_in_and_redirect(resource_name, @confirmable)
  end
end

user.rb

# /app/models/user.rb
class User < ActiveRecord::Base
  devise :database_authenticatable, :registerable,
         :recoverable, :rememberable, :trackable, :validatable, :confirmable

  attr_readonly :email
  attr_accessor :company_name
  attr_accessor :company_domain

  # removed methods needed to Override confirmations so users can pick their own passwords as part of confirmation activation
  # https://github.com/plataformatec/devise/wiki/How-To:-Override-confirmations-so-users-can-pick-their-own-passwords-as-part-of-confirmation-activation
end

user_sanitizer.rb

# /app/lib/user_sanitizer.rb
# required in an initializer
class UserParameterSanitizer < Devise::ParameterSanitizer

private
  def account_update
      default_params.permit(:first_name, :last_name, :company_name, :company_domain, :email, :password, :password_confirmation, :current_password)
  end
end