Yes you can. The method I would use is IAW the standard on applying reference designators, namely ANSI/ASME Y14.44 “Reference Designations for Electrical and Electronics Parts and Equipment”. The short of it is to use the non-class letter N (from IEEE 315, Clause 22.4) as a ref des prefix as follows: Assign N1 for your SMT parts and N2 for the THT parts. Thus you would have N1C1, N1L1, N1R1, etc. for your SMT parts and N2C1, N2L1, N2R1, etc. for your THT parts.
If you want further information on reference designations see the following:
Reference Designation of Electronic Parts
For the latest on reference designation of electronic parts see my blog posts at <www.txplore.com/blog>. Dr. Peter Dalmaris has kindly posted my seven articles on his Tech Explorations website out of Sydney, Australia. There is a main article and six appendices listed as follows:
(7) “Reference Designations For Electrical And Electronics Parts And Equipment”
Lawrence Joy
18 September, 2018
(1) “Appendix A. List of Pertinent Applicable Standards”
Lawrence Joy
20 September, 2018
(6) “Appendix B. Class Designation Letters”
Lawrence Joy
20 September, 2018
(5) “Appendix C: List of Nonconforming Class Letters”
Lawrence Joy
20 September, 2018
(4) “Appendix D. System Subdivision”
Lawrence Joy
20 September, 2018
(3) “Appendix E: KiCad Anomalous Handling of Suffix Letters”
Lawrence Joy
20 September, 2018
(2) “Appendix F: Scenario Questions and Answers”
Lawrence Joy
20 September, 2018
You should look at the main article , Nr 7, first and then the appendices. The reason the numbering is out of sequence is because the newer dated material is first, followed by the older dated material, and in order of posting. As you go down through the blog postings you will run across Appendix A first followed by Appendices F, E, D, C, and B. The main article “Reference Designations…” is last.
–Larry