AFAIK you would only actually *need* to use ISA server if you're trying to use actual filtering policies on users or groups, and your users are using terminal services. ISA is used to pass authentication information from the TS to the Websense agents. If you're not using TS, then you shouldn't need ISA at all, and in fact ISA just complicates the whole thing tenfold.
As for transparent filtering, it depends on how deep you're asking. If you're just asking in general, then there's plenty of responses here already. If you're asking "How do I configure websense for transparent filtering?" then that's a different matter.
Websense first has to be set up in your network infrastructure as a mandatory sort of gateway. It can obviously only filter traffic that goes through it. Configuration is going to vary by hardware, but if you're using Cisco routers they can be configured for filtering directly to Websense.
Within websense, you'll use various agent services to authenticate users, either the Network Agent or the Logon Agent if I remember correctly. These work to pass authentication info to Websense, and it should be transparent if you're on a domain setup and have set Websense to talk to your LDAP server.
If you don't want to actually filter based on specific policies or groups, then you can set up the default filtering service to just apply to everyone. You can tell Websense to use the default policy if it can't authenticate the individual user or computer.
As for Proxies and HTTPS filtering, that's a lot harder to set up. You basically need a switch that can mirror a port, and you have to set up a 2nd nic on the Websense server to watch the HTTPS traffic.
Notes:
1. I despise Websense. It's a house of cards to get running and keep up. Admittedly when it runs it's really powerful and hard to get around, but it seems like if you so much as look at the SQL server or ODBC connections you'll break the whole thing. It takes like 7 different services that are all interdependent.
2. I've only really worked with Websense Enterprise, to YMMV.