Before I setup my LLC I would receive payments to my personal account. So, going forward is it ok to continue with the way I receive payments, and deposit/transfer manually in the company account? Are there any legal issues?
You should receive payments payable to the LLC and deposit it to the company account, otherwise you may pierce the corporate liability protection. Mangling your personal and corporate funds may also render the liability limitation worthless. If you're in the US, you may also have problems if audited by tax authorities, especially if the LLC has its own tax return (like in California, for example).