You don't explicitly say United States, but that's the only country I know that has PACs. So I'll answer for the US.
For example, how does one distinguish between a donation from a lobbyist and another one from an employee?
This generally refers to registered lobbyists. Since the registrations are available for auditing donations, it's not actually that difficult to detect that.
How does one stop influence, for example, by a company subtly or not so subtly suggesting to many of its employees to donate to a particular candidate?
The general theory is that PAC and lobbyist contributions are themselves so corrupting that participating supports the system.
A company advising supporting a particular candidate and encouraging individual donations is considered to be less corrupting. It's harder for the company to say, look at how much we contributed if the contributions come separately without identification.
All that said, this is still possible. No system is perfect.
Finally, is there a such thing as a "local PAC"? Such as an organization whose membership is exclusively constituents of a congressman? If this kind of organization does exist, then is there something inherently wrong with accepting donations from it? (Perhaps aside from the fact that it simply blurs the lines and makes things too complicated.)
If you promise to only take small individual donations, then there is no point to taking PAC donations from local individuals. They could just make the donations directly to you. So the only reason for the PAC would be to get around the individual donation limits.
Why take contributions from something that only exists to evade the law?
Union locals often have their own PACs and some may be restricted to just one Representative's district. So this is possible, but as I said, the only point to this is to evade contribution limits. And most union members don't contribute enough for that to matter.