Hi Nishant,
You can add multiple permission sets, just that it should be inside a single Permission.xml file.
Use Generate Permission using Ctrl + Shift + P to generate
Refer below.
<?xml version="1.0" encoding="utf-8"?>
<PermissionSets>
<PermissionSet RoleID="DATA DELETION TOOL" RoleName="Data Deletion Tool">
<Permission>
<ObjectType>5</ObjectType>
<ObjectID>50190</ObjectID>
<ReadPermission>0</ReadPermission>
<InsertPermission>0</InsertPermission>
<ModifyPermission>0</ModifyPermission>
<DeletePermission>0</DeletePermission>
<ExecutePermission>1</ExecutePermission>
<SecurityFilter />
</Permission>
<Permission>
<ObjectType>0</ObjectType>
<ObjectID>50190</ObjectID>
<ReadPermission>1</ReadPermission>
<InsertPermission>1</InsertPermission>
<ModifyPermission>1</ModifyPermission>
<DeletePermission>1</DeletePermission>
<ExecutePermission>0</ExecutePermission>
<SecurityFilter />
</Permission>
</PermissionSet>
<PermissionSet RoleID="DATA DELETION TOOL2" RoleName="Data Deletion Tool2">
<Permission>
<ObjectType>5</ObjectType>
<ObjectID>50190</ObjectID>
<ReadPermission>0</ReadPermission>
<InsertPermission>0</InsertPermission>
<ModifyPermission>0</ModifyPermission>
<DeletePermission>0</DeletePermission>
<ExecutePermission>1</ExecutePermission>
<SecurityFilter />
</Permission>
<Permission>
<ObjectType>0</ObjectType>
<ObjectID>50190</ObjectID>
<ReadPermission>1</ReadPermission>
<InsertPermission>1</InsertPermission>
<ModifyPermission>1</ModifyPermission>
<DeletePermission>1</DeletePermission>
<ExecutePermission>0</ExecutePermission>
<SecurityFilter />
</Permission>
</PermissionSet>
</PermissionSets>