Denis,
I have seen Method correctly append a number to a QB custom field to avoid a naming conflict within Method table field names. I had a field named "Customer" in my Items table, and thankfully Method appended a number to this field and in every case it looks like Method protects the user from violating QB field integrity.
But, I think it is very good advice to consider a naming convention for QB custom fields as it can become very confusing to sort out fields when designing screens and reports. It could be a good idea to add a prefix or suffix to the custom field name like CUST[any custom QB name] or [any custom QB name]CUST such that it is easy to distinguish between custom fields added to QB and replicated in Method versus custom fields created in Method.
Cheers,
James