Orthogonal-time-frequency-space (OTFS) has been developed as a promising modulation scheme for high Doppler channels. In OTFS systems, channel estimation (CE) plays a key role. Most existing CE schemes put pilots in delay-Doppler (DD)-domain, often resulting in low spectrum efficiency and high peak-to-average-power-ratio (PAPR). In this paper, we propose three schemes to solve the problems. Proposed methods have distinct features being able to estimate fractional delays and fractional Dopplers. Different from existing methods, our approach places pilots in time-frequency (TF)-domain. The first scheme overlaps pilots and data in both TF- and DD-domain, while Scheme II overlaps them in TF- but not in DD-domain. To further enhance the performance, the third scheme makes pilots and data non-overlapped in both TF- and DD-domain. To conduct CE, time-domain pilot signals are extracted with a filtering operation and a two-dimensional frequency estimation problem is formulated consequently. Delays are first estimated with root-MUSIC. Then, Dopplers are estimated using a simple line-fitting method. Finally, channel gains are estimated by a least-squares method. To solve the interference between pilots and data, successive-interference-cancellation (SIC) is also applied. With the estimated channel, a minimum-mean-square-error (MMSE) equalizer is used for the compensation of channel effect. Simulation results show that the bit-error-rate (BER) performance with the channel estimated by proposed CE methods can approach to that with known channel. Also, spectrum efficiency can be improved by at most 25% and PAPR can be reduced by at least 19 dB.