Control traffic Switch cisco -> MK -> ISP

Dear all,

I actually have all interfaces from office connected to same Mikrotik and Mikrotik to ISP, its works fine, without problem. And I can control all traffic (proxy, netflow - ntopng + nprobe, torch…)

Now we need expand our office so, we have some cisco switchs, I would like to know if I can connect all employers to same switch (or different creating vlan between them), after 1 interface Switch → Mikrotik and after Mikrotik → ISP. And if I can check traffic how I can do now being all interfaces connected on Mikrotik. Maybe couldn’t I mark traffic on Mikrotik because all connections are received for same port?
Or should I use a proxy like Squid between cisco - ISP

In summary:
Switch cisco (all employers) → Mikrotik (marking all traffic between each computer - mac/ip ) → ISP.

Thanks.

Any?