Umbrella or Limited?
When you own a company, you and your company are separate legal entities, and indeed have separate bank accounts. You are employed by your company, although you would not normally have a contract of employment because you are a director of your company. The fees that you earn while on assignment belong to your company and out of these fees your company pays all its running costs. The most significant of these running costs is the salary that it pays you, and which you receive after deduction of the appropriate tax and NI. (Of course, you also own your company so you may also pay yourself dividends out of the profits).
When you work for an umbrella company, because you are not a director, you enter into a contract of employment and so become an employee of the umbrella company. The fees you earn while on assignment belong to the umbrella company, which in turn pays you a salary.
You will therefore understand that working as an employee of your own company and working as an employee of an umbrella company are two completely separate and unrelated activities. It follows that the expenses incurred in running your company may be set off only against the income of your company, and the expenses you incur while working through the umbrella company may be claimed only from the umbrella company.