Hi @MukeshAEM,
Tools > General > GraphQL Query Editor is available only in AEM as a Cloud Service, this is a bit different editor comparing to the one that is provided as part of graphiql-0.0.6.zip. Also if you will look into urls they are different as well:
- AEM 6.5 editor is part of add-on additional package and is available under /content/graphiql.html
- AEM as a Cloud Service editor is part of AEM (it is build in) and is exposed under /aem/graphiql.html
If for any reason you still would like to have an editor link available from Tools section you can simply overlay /libs/cq/core/content/nav/tools/general and add below node under general node:
<graphiql
jcr:primaryType="nt:unstructured"
href="/content/graphiql.html"
icon="branch2"
id="cq-sites-graphiql"
jcr:description="Create, simulate and manage GraphQL queries, including persisted queries in AEM"
jcr:title="GraphQL Query Editor"/>

and the result on AEM 6.5

Here is also a link to the documentation that describes console customization:
Regarding your second question, there is no Persisted Query option available from GUI. However you can always use Postman or similar tool to create Persisted Query. You have to make sure that you have enabled Persisted Queries on your endpoint level. Please find step by step instruction under below 2 links: