Procedure is clearly mentioned by IQAS in how to apply section. Link:
https://www.alberta.ca/iqas-immigration-apply.aspx
Procedure would be as follows:
( I have assumed you are from India. Country specific details available @
https://www.alberta.ca/assets/documents/iqas/eca-required-documents.pdf
)
For each credential, you need to have Degree Certificate awarded by the university and transcript and/or statement of marks attested by the university.
Photocopy of degree certificate can be uploaded by the applicant or applicant can mail it to them.
However, transcript and statement of mark along with request form (attested by university) should be directly sent by the university.
So
you will have to mail them completed application with signature, both degree/credential certificates and name change proof if any. I would suggest also to include covering letter explaining what you have included in the mail.
And
each board/university should send sealed envelope with Attested request form, transcript and/or statement of marks
directly to IQAS. IQAS will not accept if you send attested request form, transcript and/or statement of marks.
So in your case there will be three mails to IQAS.
1. Sent by you. This will include singed application form and other documents that you are supposed to send.
2. Sent by First University: Transcript and/or Statement of marks for first credential
3. Sent by Second University: Transcript and/or statement of marks for second credential
Even I am planing to send my two credentials from different universities to IQAS for evaluation. I am not sending to WES because they do not evaluate credentials from one of my universities (SCDL)
Hope this helps.