We have used a low repetition rate (1 kHz), femtosecond laser amplifier in combination with a spatial light modulator (SLM) to write optical waveguides with controllable cross-section inside a phosphate glass sample. The SLM is used to induce a controllable amount of astigmatism in the beam wavefront while the beam ellipticity is controlled through the propagation distance from the SLM to the focusing optics of the writing set-up. The beam astigmatism leads to the formation of two separate disk-shaped foci lying in orthogonal planes. Additionally, the ellipticity has the effect of enabling control over the relative peak irradiances of the two foci, making it possible to bring the peak irradiance of one of them below the material transformation threshold. This allows producing a single waveguide with controllable cross-section. Numerical simulations of the irradiance distribution at the focal region under different beam shaping conditions are compared to in situ obtained experimental plasma emission images and structures produced inside the glass, leading to a very satisfactory agreement. Finally, guiding structures with controllable cross-section are successfully produced in the phosphate glass using this approach.