Not sure what you mean by "declare my vlans in both switches".
The automatic update of the vlan database on each switch is done by VTP, assuming you are using VTP Server/Client setup. VTP is not dependant on the trunk encapsulation ie. it will work over ISL or 802.1q.
So it is not a property of ISL it is VTP which will also work with 802.1q.
Basically what you have currently is trunk link using isl as the encapsulation and all vlans are allowed across the trunk because you have not manually pruned off any vlans on the trunk , if you change to dot1q nothing really changes other than the trunk encapsulation which will then be dot1q. Maybe you can explain what you mean by "declare my vlans" in both switches.
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