Suppose you have a column in in your table as "SelectedFlag" as char datatype. And you are storing 'Y' or 'N' as per your requirement. Now you have to modify your select statement like
"select col1, col2, cast( (case when SelectedFlag='Y' then 1
when SelectedFlag = 'N' then 0 end) as bit) as SelectedFlag from
Table1"
in GridView
<asp:TemplateField HeaderText="Select">
<ItemTemplate>
<asp:CheckBox ID="ChkSelect"
runat="server"
Checked='<%# Eval("SelectedFlag") %>' />
</ItemTemplate>
</asp:TemplateField>
It will automatically check/uncheck your checkbox inside girdview based on your database.